I'm unsure as to how I had done it, but in one of my forts I had troglodytes listed as citizens. It was unmodded and I had a troglodyte breeding room (I don't know why); I think I may have retired and rejoined the fort which bugged the save.
I made the troglodytes tavern keepers and such to leave my dwarves for more important jobs.
I just had a look but I couldn't find any pictures, but I'm certain I wasn't just hallucinating.
I can diagnose this i think, implicitly the troglodytes born on the map belong to your 'site' because they are intelligent (intelligent creature birth rules, whever the baby lands its yours, if offsite its theirs), but since they are animals they emigrate off, the whole wacky allocation to check for fortress citizens probably saw 'intelligent being = born on site, add to citizens' without context, so validated the troglodytes.
However, this is a bug because semi-sapients were fixed in a prior version to not be applicable for occupation jobs (after modders accessed it with pet tags), this somehow this bypasses the code Toady put in blocking it, if it can be recreated and uploaded to Mantis for a hopeful fix it might be useful.