Managed to produce the issue with constant error spam and missing assets when working in a prefab and then backing out into the scene. The following error keeps repeating forever if the "Auto refresh" option on the generator is checked. "MyPrefab" is the prefab that is placed in the scene, and it contains a generator in one of its child objects
Code:
ArgumentException: Could not load Prefab contents at path MyPrefab.prefab. Prefabs should have exactly 1 root GameObject, 2 was found.
UnityEditor.PrefabUtility.LoadPrefabContents (System.String assetPath) (at <5e6ebaa7d75c4d5399dc81ecead6b43f>:0)
FluffyUnderware.Curvy.Generator.CurvyGenerator.DeleteAllOutputManagedResourcesFromAssociatedPrefab () (at Assets/3rdParty/ToolBuddy/Assets/Curvy/Scripts/CG/CurvyGenerator.cs:1217)
FluffyUnderware.Curvy.Generator.CGModule.TryDeleteChildrenFromAssociatedPrefab () (at Assets/3rdParty/ToolBuddy/Assets/Curvy/Scripts/CG/CGModule.cs:756)
FluffyUnderware.Curvy.Generator.Modules.CreateMesh.Refresh () (at Assets/3rdParty/ToolBuddy/Assets/Curvy/Scripts/CG Modules/CreateMesh.cs:822)
FluffyUnderware.Curvy.Generator.CGModule.doRefresh () (at Assets/3rdParty/ToolBuddy/Assets/Curvy/Scripts/CG/CGModule.cs:778)
FluffyUnderware.Curvy.Generator.CurvyGenerator.Refresh (System.Boolean forceUpdate) (at Assets/3rdParty/ToolBuddy/Assets/Curvy/Scripts/CG/CurvyGenerator.cs:851)
FluffyUnderware.Curvy.Generator.CurvyGenerator.TryAutoRefresh () (at Assets/3rdParty/ToolBuddy/Assets/Curvy/Scripts/CG/CurvyGenerator.cs:882)
FluffyUnderware.Curvy.Generator.CurvyGenerator.Update () (at Assets/3rdParty/ToolBuddy/Assets/Curvy/Scripts/CG/CurvyGenerator.cs:312)
FluffyUnderware.Curvy.Generator.CurvyGenerator.editorUpdate () (at Assets/3rdParty/ToolBuddy/Assets/Curvy/Scripts/CG/CurvyGenerator.cs:299)
UnityEditor.EditorApplication.Internal_CallUpdateFunctions () (at <5e6ebaa7d75c4d5399dc81ecead6b43f>:0)