There's no safeguards--it is a powerful feature to support multiple catalogs at the same time, but it can cause unintended duplicates. Either be aware of what catalogs are active for add/modify or use a single catalog. The catalog system doesn't second-guess your intentions.
We could add a confirmation box for when multiple catalogs are selected to be added/modified, but some may find that intrusive. A preference could be added to turn the warnings off.
-Kirk