Steps to repro:
- Launch the attached project
- Load the placeholder scene from the scenes folder
- Now add the Zone1 scene additively
- Expand Zone1 and drag and drop the Fox_model GO to the placeholder scene

Unity crashes with the following stacktrace
Launching bug reporter
Obtained 55 stack frames.
#0 0x000001019a3d37 in DetectCrossSceneReferencesAndPrintWarnings(UnityScene*)
#1 0x00000101a5850e in DragAndDropForwarding::ForwardDragAndDrop(Object*, DragAndDropForwarding::DragInfo*)
#2 0x000001024a8c7e in InternalEditorUtility_CUSTOM_HierarchyWindowDrag(MonoObject*, unsigned char, HierarchyDropMode)
#3 0x0000010b6f0c75 in (wrapper managed-to-native) UnityEditorInternal.InternalEditorUtility:HierarchyWindowDrag (UnityEditor.HierarchyProperty,bool,UnityEditorInternal.InternalEditorUtility/HierarchyDropMode) + 0xa5 (0x10b6f0bd0 0x10b6f0ca4) [0x10ef47990 - Unity Child Domain]
#4 0x0000010b648c68 in UnityEditor.GameObjectsTreeViewDragging:DoDrag (UnityEditor.TreeViewItem,UnityEditor.TreeViewItem,bool,UnityEditor.TreeViewDragging/DropPosition) + 0x4e8 (0x10b648780 0x10b648c77) [0x10ef47990 - Unity Child Domain]

The crash does not happen on 5.3.1p2 and in 5.4.0b2. Seems to have been introduced after the crossreference check

Note this can be reproduced with a simple prefab instance that is not a root in the hierarchy. Drag that to another scene and it crashes