This problem still exists.
I had two groups.
I deleted one probuilder object before removing it from the group, and unity was full of this errors:
NullReferenceException: Object reference not set to an instance of an object ProGroups.Group.<RemoveNullOrEmpty>m__F (UnityEngine.GameObject x) (at Assets/ProCore/ProGroups/Scripts/InScene/GroupContainer.cs:35) System.Linq.Enumerable+<CreateWhereIterator>c__Iterator1D`1[unityEngine.GameObject].MoveNext () System.Collections.Generic.List`1[unityEngine.GameObject].AddEnumerable (IEnumerable`1 enumerable) (at /Users/builduser/buildslave/mono/build/mcs/class/corlib/System.Collections.Generic/List.cs:128) System.Collections.Generic.List`1[unityEngine.GameObject]..ctor (IEnumerable`1 collection) (at /Users/builduser/buildslave/mono/build/mcs/class/corlib/System.Collections.Generic/List.cs:65) System.Linq.Enumerable.ToArray[GameObject] (IEnumerable`1 source) ProGroups.Group.RemoveNullOrEmpty () (at Assets/ProCore/ProGroups/Scripts/InScene/GroupContainer.cs:35) ProGroups.GroupContainer.Clean () (at Assets/ProCore/ProGroups/Scripts/InScene/GroupContainer.cs:308) ProGroups.ProGroups_Window.OnGUI () (at Assets/ProCore/ProGroups/Scripts/Editor/ProGroups_Window.cs:275) System.Reflection.MonoMethod.Invoke (System.Object obj, BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object parameters, System.Globalization.CultureInfo culture) (at /Users/builduser/buildslave/mono/build/mcs/class/corlib/System.Reflection/MonoMethod.cs:222)
After that the ProGroups window crashed as soon as i opened it, and didn't show the groups, it just hang.
I've upgraded to the latest version (deleted the previous version first). I'm using Unity 5.3.5
I've used the menu option "Clear all groups in scene" and it seems that the errors are gone.
But now the ProGroups window does not open. I've deleted ProGroups, restarted Unity, re-imported it, and nothing.