I've had that happen a few times, usually there's one remaining enemy that's trapped on a few props. I'll look over the enemy handling code regardless. Also, I'm planning on adding a visual indicator that points to the last two or three enemies in a room to avoid this kind of situation.
I cleared all the props in the rooms the times that I encountered that, like destroying all crates and barrels that I could find, but I still did not find the last enemy.