Twenty Fifteen Theme and only BuddyPress activated and I still get that message.
… Disable BuddyPress the error is gone. Custom Taxonomy and Post types were made via the functions.php, as of my testing with the Twenty Fifteen these customizations were not enabled at all. Now I think I did forget to mention this is a multisite setup with only 1 site currently.
Can you give me some clues of what hooks might have been used? I can do some investigating.