Been getting this error consistently after porting to Unity 5 even after various fixes to other aspect that were broken after the port, although it does not seem to be whats causing the problems. From the looks of it it may be an editor (UI?) bug or trigger based collider bug (feels more like a warning than an error as it does not break play mode).
There really should be an option to submit bug reports to let Unity know about that kind of issue. Wouldn’t it be fantastic if there was some option like “Help → Submit a Bug”?
Did you guys ever figure out why you get this error? I also get it when changing scenes. For me, it only happens when I’ve got certain assets maintaining their state between scenes. I don’t see any negative effects from it, it just spams in my console a couple dozen times.