diff --git a/web/app/components/header/index.tsx b/web/app/components/header/index.tsx
index 560d5f1eaa..2c1f3ca32e 100644
--- a/web/app/components/header/index.tsx
+++ b/web/app/components/header/index.tsx
@@ -42,10 +42,17 @@ const Header = () => {
     else
       setShowAccountSettingModal({ payload: ACCOUNT_SETTING_TAB.BILLING })
   }, [isFreePlan, setShowAccountSettingModal, setShowPricingModal])
+  const handleDownloadGraphImportLog = useCallback(() => {
+    void import('@/app/components/workflow/collaboration/core/collaboration-manager')
+      .then(({ collaborationManager }) => {
+        collaborationManager.downloadGraphImportLog()
+      })
+      .catch(() => {})
+  }, [])
 
   const renderLogo = () => (
     <h1>
-      <Link href="/apps" className="flex h-8 shrink-0 items-center justify-center overflow-hidden whitespace-nowrap px-0.5 indent-[-9999px]">
+      <Link href="/apps" className="flex h-8 shrink-0 items-center justify-center overflow-hidden px-0.5 indent-[-9999px] whitespace-nowrap">
         {isBrandingEnabled && systemFeatures.branding.application_title ? systemFeatures.branding.application_title : 'Dify'}
         {systemFeatures.branding.enabled && systemFeatures.branding.workspace_logo
           ? (
@@ -91,7 +98,7 @@ const Header = () => {
 
   return (
     <div className="flex h-[56px] items-center">
-      <div className="flex min-w-0 flex-1 items-center pl-3 pr-2 min-[1280px]:pr-3">
+      <div className="flex min-w-0 flex-1 items-center pr-2 pl-3 min-[1280px]:pr-3">
         {renderLogo()}
         <div className="mx-1.5 shrink-0 font-light text-divider-deep">/</div>
         <WorkspaceProvider>
@@ -105,7 +112,15 @@ const Header = () => {
         {(isCurrentWorkspaceEditor || isCurrentWorkspaceDatasetOperator) && <DatasetNav />}
         {!isCurrentWorkspaceDatasetOperator && <ToolsNav className={navClassName} />}
       </div>
-      <div className="flex min-w-0 flex-1 items-center justify-end pl-2 pr-3 min-[1280px]:pl-3">
+      <div className="flex min-w-0 flex-1 items-center justify-end pr-3 pl-2 min-[1280px]:pl-3">
+        <button
+          type="button"
+          data-testid="workflow-import-log-download"
+          className="top-1/2 left-full ml-1 h-3 w-3 -translate-y-1/2 opacity-0"
+          aria-hidden="true"
+          tabIndex={-1}
+          onClick={handleDownloadGraphImportLog}
+        />
         <EnvNav />
         <div className="mr-2">
           <PluginsNav />
diff --git a/web/app/components/workflow/collaboration/core/collaboration-manager.ts b/web/app/components/workflow/collaboration/core/collaboration-manager.ts
index 07d0bddb01..d60cfe9da0 100644
--- a/web/app/components/workflow/collaboration/core/collaboration-manager.ts
+++ b/web/app/components/workflow/collaboration/core/collaboration-manager.ts
@@ -78,7 +78,32 @@ type GraphImportLogEntry = {
   }
 }
 
+type SetNodesAnomalyReason = 'node_count_decrease' | 'start_removed'
+
+type SetNodesAnomalyLogEntry = {
+  timestamp: number
+  appId: string | null
+  source: string
+  reasons: SetNodesAnomalyReason[]
+  oldCount: number
+  newCount: number
+  removedNodeIds: string[]
+  oldStartNodeIds: string[]
+  newStartNodeIds: string[]
+  oldNodeIds: string[]
+  newNodeIds: string[]
+  visibilityState: DocumentVisibilityState | 'unknown'
+  meta: {
+    leaderId: string | null
+    isLeader: boolean
+    graphViewActive: boolean | null
+    pendingInitialSync: boolean
+    isConnected: boolean
+  }
+}
+
 const GRAPH_IMPORT_LOG_LIMIT = 20
+const SET_NODES_ANOMALY_LOG_LIMIT = 100
 
 const toLoroValue = (value: unknown): Value => cloneDeep(value) as Value
 const toLoroRecord = (value: unknown): Record<string, Value> => cloneDeep(value) as Record<string, Value>
@@ -102,6 +127,7 @@ export class CollaborationManager {
   private pendingGraphImportEmit = false
   private graphViewActive: boolean | null = null
   private graphImportLogs: GraphImportLogEntry[] = []
+  private setNodesAnomalyLogs: SetNodesAnomalyLogEntry[] = []
   private pendingImportLog: {
     timestamp: number
     sources: Set<'nodes' | 'edges'>
@@ -391,7 +417,7 @@ export class CollaborationManager {
     this.connect(appId, reactFlowStore)
   }
 
-  setNodes = (oldNodes: Node[], newNodes: Node[]): void => {
+  setNodes = (oldNodes: Node[], newNodes: Node[], source = 'collaboration-manager:setNodes'): void => {
     if (!this.doc)
       return
 
@@ -399,6 +425,7 @@ export class CollaborationManager {
     if (this.isUndoRedoInProgress)
       return
 
+    this.captureSetNodesAnomaly(oldNodes, newNodes, source)
     this.syncNodes(oldNodes, newNodes)
     this.doc.commit()
   }
@@ -480,8 +507,9 @@ export class CollaborationManager {
         if (value?.value && typeof value.value === 'object' && 'selectedNodeId' in value.value && this.reactFlowStore) {
           const selectedNodeId = (value.value as { selectedNodeId?: string | null }).selectedNodeId
           if (selectedNodeId) {
-            const { setNodes } = this.reactFlowStore.getState()
-            const nodes = this.reactFlowStore.getState().getNodes()
+            const state = this.reactFlowStore.getState()
+            const { setNodes } = state
+            const nodes = state.getNodes()
             const newNodes = nodes.map((n: Node) => ({
               ...n,
               data: {
@@ -489,6 +517,7 @@ export class CollaborationManager {
                 selected: n.id === selectedNodeId,
               },
             }))
+            this.captureSetNodesAnomaly(nodes, newNodes, 'reactflow-native:undo-redo-selection-restore')
             setNodes(newNodes)
           }
         }
@@ -791,9 +820,11 @@ export class CollaborationManager {
         requestAnimationFrame(() => {
           // Get ReactFlow's native setters, not the collaborative ones
           const state = reactFlowStore.getState()
+          const previousNodes = state.getNodes()
           const updatedNodes = Array.from(this.nodesMap?.values() || []) as Node[]
           const updatedEdges = Array.from(this.edgesMap?.values() || []) as Edge[]
           // Call ReactFlow's native setters directly to avoid triggering collaboration
+          this.captureSetNodesAnomaly(previousNodes, updatedNodes, 'reactflow-native:undo-apply')
           state.setNodes(updatedNodes)
           state.setEdges(updatedEdges)
 
@@ -831,9 +862,11 @@ export class CollaborationManager {
         requestAnimationFrame(() => {
           // Get ReactFlow's native setters, not the collaborative ones
           const state = reactFlowStore.getState()
+          const previousNodes = state.getNodes()
           const updatedNodes = Array.from(this.nodesMap?.values() || []) as Node[]
           const updatedEdges = Array.from(this.edgesMap?.values() || []) as Edge[]
           // Call ReactFlow's native setters directly to avoid triggering collaboration
+          this.captureSetNodesAnomaly(previousNodes, updatedNodes, 'reactflow-native:redo-apply')
           state.setNodes(updatedNodes)
           state.setEdges(updatedEdges)
 
@@ -972,6 +1005,7 @@ export class CollaborationManager {
             })
 
           // Call ReactFlow's native setter directly to avoid triggering collaboration
+          this.captureSetNodesAnomaly(previousNodes, updatedNodes, 'reactflow-native:import-nodes-map-subscribe')
           state.setNodes(updatedNodes)
 
           this.scheduleGraphImportEmit()
@@ -1067,17 +1101,37 @@ export class CollaborationManager {
 
   clearGraphImportLog(): void {
     this.graphImportLogs = []
+    this.setNodesAnomalyLogs = []
     this.pendingImportLog = null
   }
 
   downloadGraphImportLog(): void {
-    if (this.graphImportLogs.length === 0)
-      return
-
+    const reactFlowState = this.reactFlowStore?.getState()
     const payload = {
       appId: this.currentAppId,
       generatedAt: new Date().toISOString(),
       entries: this.graphImportLogs,
+      setNodesAnomalies: this.setNodesAnomalyLogs,
+      summary: {
+        logCount: this.graphImportLogs.length,
+        setNodesAnomalyCount: this.setNodesAnomalyLogs.length,
+        leaderId: this.leaderId,
+        isLeader: this.isLeader,
+        graphViewActive: this.graphViewActive,
+        pendingInitialSync: this.pendingInitialSync,
+        isConnected: this.isConnected(),
+        hasDoc: Boolean(this.doc),
+        hasReactFlowStore: Boolean(this.reactFlowStore),
+        onlineUsersCount: this.onlineUsers.length,
+        crdtCounts: {
+          nodes: this.getNodes().length,
+          edges: this.getEdges().length,
+        },
+        reactFlowCounts: {
+          nodes: reactFlowState?.getNodes().length ?? 0,
+          edges: reactFlowState?.getEdges().length ?? 0,
+        },
+      },
     }
     const stamp = new Date().toISOString().replace(/[:.]/g, '-')
     const appSuffix = this.currentAppId ?? 'unknown'
@@ -1091,6 +1145,54 @@ export class CollaborationManager {
     URL.revokeObjectURL(url)
   }
 
+  private captureSetNodesAnomaly(oldNodes: Node[], newNodes: Node[], source: string): void {
+    const oldNodeIds = oldNodes.map(node => node.id)
+    const newNodeIds = newNodes.map(node => node.id)
+    const newNodeIdSet = new Set(newNodeIds)
+    const removedNodeIds = oldNodeIds.filter(nodeId => !newNodeIdSet.has(nodeId))
+
+    const oldStartNodeIds = oldNodes
+      .filter(node => (node.data as CommonNodeType | undefined)?.type === 'start')
+      .map(node => node.id)
+    const newStartNodeIds = newNodes
+      .filter(node => (node.data as CommonNodeType | undefined)?.type === 'start')
+      .map(node => node.id)
+
+    const reasons: SetNodesAnomalyReason[] = []
+    if (newNodes.length < oldNodes.length)
+      reasons.push('node_count_decrease')
+    if (oldStartNodeIds.length > 0 && newStartNodeIds.length === 0)
+      reasons.push('start_removed')
+
+    if (!reasons.length)
+      return
+
+    const entry: SetNodesAnomalyLogEntry = {
+      timestamp: Date.now(),
+      appId: this.currentAppId,
+      source,
+      reasons,
+      oldCount: oldNodes.length,
+      newCount: newNodes.length,
+      removedNodeIds,
+      oldStartNodeIds,
+      newStartNodeIds,
+      oldNodeIds,
+      newNodeIds,
+      visibilityState: typeof document === 'undefined' ? 'unknown' : document.visibilityState,
+      meta: {
+        leaderId: this.leaderId,
+        isLeader: this.isLeader,
+        graphViewActive: this.graphViewActive,
+        pendingInitialSync: this.pendingInitialSync,
+        isConnected: this.isConnected(),
+      },
+    }
+    this.setNodesAnomalyLogs.push(entry)
+    if (this.setNodesAnomalyLogs.length > SET_NODES_ANOMALY_LOG_LIMIT)
+      this.setNodesAnomalyLogs.splice(0, this.setNodesAnomalyLogs.length - SET_NODES_ANOMALY_LOG_LIMIT)
+  }
+
   private snapshotReactFlowGraph(): { nodes: Node[], edges: Edge[] } {
     if (!this.reactFlowStore) {
       return {
diff --git a/web/app/components/workflow/hooks/use-collaborative-workflow.ts b/web/app/components/workflow/hooks/use-collaborative-workflow.ts
index 9d019f981f..267bb2ecb3 100644
--- a/web/app/components/workflow/hooks/use-collaborative-workflow.ts
+++ b/web/app/components/workflow/hooks/use-collaborative-workflow.ts
@@ -39,13 +39,14 @@ export const useCollaborativeWorkflow = () => {
   const store = useStoreApi()
   const { setNodes: collabSetNodes, setEdges: collabSetEdges } = collaborationManager
 
-  const setNodes = useCallback((newNodes: Node[], shouldBroadcast: boolean = true) => {
+  const setNodes = useCallback((newNodes: Node[], shouldBroadcast: boolean = true, source = 'use-collaborative-workflow:setNodes') => {
     const { getNodes, setNodes: reactFlowSetNodes } = store.getState()
     if (shouldBroadcast) {
       const oldNodes = getNodes()
       collabSetNodes(
         oldNodes.map(sanitizeNodeForBroadcast),
         newNodes.map(sanitizeNodeForBroadcast),
+        source,
       )
     }
     reactFlowSetNodes(newNodes)
diff --git a/web/app/components/workflow/hooks/use-leader-restore.ts b/web/app/components/workflow/hooks/use-leader-restore.ts
index 5e47f025df..fb050641c8 100644
--- a/web/app/components/workflow/hooks/use-leader-restore.ts
+++ b/web/app/components/workflow/hooks/use-leader-restore.ts
@@ -45,7 +45,7 @@ export const usePerformRestore = () => {
     const currentNodes = collaborationManager.getNodes()
     const currentEdges = collaborationManager.getEdges()
 
-    collaborationManager.setNodes(currentNodes, nodes)
+    collaborationManager.setNodes(currentNodes, nodes, 'leader-restore:apply-graph')
     collaborationManager.setEdges(currentEdges, edges)
     collaborationManager.refreshGraphSynchronously()
 
diff --git a/web/app/components/workflow/hooks/use-nodes-interactions.ts b/web/app/components/workflow/hooks/use-nodes-interactions.ts
index 815b4ecc60..7c97025fd6 100644
--- a/web/app/components/workflow/hooks/use-nodes-interactions.ts
+++ b/web/app/components/workflow/hooks/use-nodes-interactions.ts
@@ -627,7 +627,6 @@ export const useNodesInteractions = () => {
   )
 
   const { deleteNodeInspectorVars } = useInspectVarsCrud()
-
   const handleNodeDelete = useCallback(
     (nodeId: string) => {
       if (getNodesReadOnly())
@@ -766,7 +765,7 @@ export const useNodesInteractions = () => {
         })
         draft.splice(currentNodeIndex, 1)
       })
-      setNodes(newNodes)
+      setNodes(newNodes, true, 'nodes:perform-batch-cascade-delete')
       const newEdges = produce(edges, (draft) => {
         return draft.filter(
           edge =>
@@ -2116,7 +2115,7 @@ export const useNodesInteractions = () => {
 
     const shouldBroadcast = collaborationManager.isConnected()
     setEdges(edges, shouldBroadcast)
-    setNodes(nodes, shouldBroadcast)
+    setNodes(nodes, shouldBroadcast, 'nodes:history-back')
     if (shouldBroadcast)
       collaborationManager.emitHistoryAction('undo')
     workflowStore.setState({ edgeMenu: undefined })
@@ -2141,7 +2140,7 @@ export const useNodesInteractions = () => {
 
     const shouldBroadcast = collaborationManager.isConnected()
     setEdges(edges, shouldBroadcast)
-    setNodes(nodes, shouldBroadcast)
+    setNodes(nodes, shouldBroadcast, 'nodes:history-forward')
     if (shouldBroadcast)
       collaborationManager.emitHistoryAction('redo')
     workflowStore.setState({ edgeMenu: undefined })