diff --git a/packages/bundlers/default/src/DefaultBundler.js b/packages/bundlers/default/src/DefaultBundler.js
index 32952d99b84..7967da65b16 100644
--- a/packages/bundlers/default/src/DefaultBundler.js
+++ b/packages/bundlers/default/src/DefaultBundler.js
@@ -141,7 +141,10 @@ export default new Bundler({
           let assets = bundleGraph.getDependencyAssets(dependency);
 
           for (let asset of assets) {
-            if (bundleGraph.isAssetInAncestorBundles(bundle, asset)) {
+            if (
+              bundle.hasAsset(asset) &&
+              bundleGraph.isAssetInAncestorBundles(bundle, asset)
+            ) {
               bundleGraph.removeAssetGraphFromBundle(asset, bundle);
             }
           }
diff --git a/packages/core/core/src/BundleGraph.js b/packages/core/core/src/BundleGraph.js
index 53e9f116ada..2f4f1b4af92 100644
--- a/packages/core/core/src/BundleGraph.js
+++ b/packages/core/core/src/BundleGraph.js
@@ -103,11 +103,14 @@ export default class BundleGraph {
 
   removeAssetGraphFromBundle(asset: Asset, bundle: Bundle) {
     this._graph.removeEdge(bundle.id, asset.id);
-    this._graph.traverse(node => {
-      if (node.type === 'asset' || node.type === 'dependency') {
+    this.traverseBundle(
+      bundle,
+      node => {
         this._graph.removeEdge(bundle.id, node.id, 'contains');
-      }
-    }, nullthrows(this._graph.getNode(asset.id)));
+      },
+      false,
+      nullthrows(this._graph.getNode(asset.id))
+    );
   }
 
   createAssetReference(dependency: Dependency, asset: Asset): void {
@@ -388,7 +391,8 @@ export default class BundleGraph {
   traverseBundle<TContext>(
     bundle: Bundle,
     visit: GraphVisitor<AssetNode | DependencyNode, TContext>,
-    includeAll: boolean = false
+    includeAll: boolean = false,
+    startNode?: BundleGraphNode
   ): ?TContext {
     return this._graph.filteredTraverse(
       (node, actions) => {
@@ -408,7 +412,7 @@ export default class BundleGraph {
         actions.skipChildren();
       },
       visit,
-      nullthrows(this._graph.getNode(bundle.id))
+      startNode ?? nullthrows(this._graph.getNode(bundle.id))
     );
   }