Are you merging in the Duplicate Items view or via a search? I believe there's an issue, which we haven't been able to reproduce, where the search bar ends up showing items from multiple libraries, and if you try to merge those you'll get an error. (If you're seeing that, you can try disabling BBT to see if it still happens.) This won't happen in the Duplicate Items view.

Beyond that, check your database integrity from the Advanced → Files and Folders pane of the Zotero preferences.