Korgoth said:...
The dungeon is an alien realm inimical to surfaceworlders. So the party had better bring their "A" game if they want to survive. But a big part of the A-game is thinking rationally. So, as others have pointed out as well, if you have a room with a monster that seems very unlikely, or two monsters in proximity that seem an unlikely pair, there needs to be some rationale for it because you want to get your players into the habit of asking those questions... which means there will need to be satisfactory answers. However, there's nothing to say that those answers have to be evident at the time. ....
Exactly! I find this half the fun when designing a dungeon and actually enjoy starting off with some random population of monsters and coming up with some rationale for it.