diff --git a/api/core/workflow/graph_engine/entities/graph.py b/api/core/workflow/graph_engine/entities/graph.py
index 16bf80f34a..48ae33f29a 100644
--- a/api/core/workflow/graph_engine/entities/graph.py
+++ b/api/core/workflow/graph_engine/entities/graph.py
@@ -508,11 +508,17 @@ class Graph(BaseModel):
                         branch_node_id != branch_node_id2 
                         and node_id in inner_route2
                         and len(reverse_edge_mapping.get(node_id, [])) > 1
+                        and cls._is_node_in_routes(
+                            reverse_edge_mapping=reverse_edge_mapping,
+                            start_node_id=node_id,
+                            routes_node_ids=routes_node_ids
+                        )
                     ):
                         if node_id not in merge_branch_node_ids:
                             merge_branch_node_ids[node_id] = []
 
-                        merge_branch_node_ids[node_id].append(branch_node_id2)
+                        if branch_node_id2 not in merge_branch_node_ids[node_id]:
+                            merge_branch_node_ids[node_id].append(branch_node_id2)
 
         # sorted merge_branch_node_ids by branch_node_ids length desc
         merge_branch_node_ids = dict(sorted(merge_branch_node_ids.items(), key=lambda x: len(x[1]), reverse=True))
@@ -596,6 +602,28 @@ class Graph(BaseModel):
                     routes_node_ids=routes_node_ids
                 )
 
+    @classmethod
+    def _is_node_in_routes(cls,
+                           reverse_edge_mapping: dict[str, list[GraphEdge]],
+                           start_node_id: str,
+                           routes_node_ids: dict[str, list[str]]) -> bool:
+        """
+        Recursively check if the node is in the routes
+        """
+        if start_node_id not in reverse_edge_mapping:
+            return False
+        
+        all_routes_node_ids = []
+        for _, node_ids in routes_node_ids.items():
+            for node_id in node_ids:
+                all_routes_node_ids.append(node_id)
+        
+        for graph_edge in reverse_edge_mapping[start_node_id]:
+            if graph_edge.source_node_id not in all_routes_node_ids:
+                return False
+            
+        return True
+
     @classmethod
     def _is_node2_after_node1(
         cls,