"Can't Destroy Transform Component" In MergeManagerScene.InitializeMerge()

[randomPoison]

When I try to merge a scene, I get a bunch of errors that look like the following:

Can't destroy Transform component of 'polySurface10'. If you want to destroy the game object, please call 'Destroy' on the game object instead. Destroying the transform component is not allowed.
UnityEditor.EditorApplication:OpenScene(String)
GitMerge.MergeManagerScene:InitializeMerge() (at Assets/GitMerge/Editor/MergeManagerScene.cs:25)
GitMerge.GitMergeWindow:OnGUISceneTab() (at Assets/GitMerge/Editor/GitMergeWindow.cs:128)
GitMerge.GitMergeWindow:OnGUI() (at Assets/GitMerge/Editor/GitMergeWindow.cs:104)
UnityEditor.DockArea:OnGUI()

I tried looking into why this is happening, but I can't find anyone saying why EditorApplication.OpenScene() would cause these errors. Also, these errors also don't prevent the merge from taking place, though they might be indicative of some other problems.

[FlaShG]

This sounds like a Unity bug to me. Which version are you using? Since I never ran into this, can you break down the scene to a small, reproducible example?

[randomPoison]

I'm running 4.6.2. I'll see about finding a trivial repro case.

[TheXRMonk]

Just tried the recent tool. This is still happening. Along with Can't remove (Component) because (Script) depends on it. This repo looks updated but is this tool even working?

[FlaShG]

@VirsabiMunk It's an open source tool that happily accepts contributions. I can spend some time for maintaining, but I currently don't have the time to bug hunting. I know of quite a few people who are using the tool just fine despite its present issues, which need some outside help to be tackled.