Is it possible in some levels, some monsters get stuck outside the levels? as they used to do in Doom? I remember Doom had some bugs where the monsters (especially lost souls) would somehow end up outside levels.. and are stuck there... they only way to kill them is if one noclips outside and kill them within the blocking.

Does this happen in Quake too? Maybe to the fishes?

There's one level E2M3: The Crypt of Decay where I just cannot find the last 5 monters. I've searched everywhere and got all secrets. Problem is, am playing the PSP Quake version and it doesn't have cheats.

Yes. I don't know specifics, but I do remember reading about this at http://speeddemosarchive.com/forum/ (the quake section ofcourse).

These speedrunner guys know all there is to know about this kind of singleplayer stuff.

There is a bug with the fishes in Quake. Each fish counts twice for the total monster count (bug) but if you kill one it only counts once (correct).