Steps to replicate:
- Start a mission that's "infected" with 2 monsters (I had some really bad luck).

- Kill both monsters and collect trophies

- Fail to beat the final non-monster task (without choosing to resign? Not sure if this is important)

- When you go back to the main screen, the second monster you killed will not have been removed from the adventure

This basically stopped me from completing certain missions and lost me a game. (Went down to the wire! )

I experienced the same problem several times too. Initially I thought that the one-monster-surviving thing was part of the game mechanics.