One possible scenario that would lead to this message:
If user A has the layers reserved, user B can still create a new layer and start using it. (You don't have to have layers reserved to create a new layer). However, when user B sends his/her changes, than this warning will appear, since the layer combinations on the server have to be updated with the new layer's information.
Gergely Kmethy
VP, Customer Success, Graphisoft