I've played through the level numerous times and there are always 2 enemies that I can't find. Always 55/57. I'm not sure if the level is bugged or not. I've verified game cache on steam as well as reinstalled the game.

I'm fairly certain i've checked every location. I've ran back through the entire level after beating each part of it, and they just don't seem to exist.

It also happens on r1m6. 47/48

Any suggestions on a fix?

if you're still looking for the answer, 55 and 47 are the max amount of kills in these levels. i suggest using joequake and doestats. they have these fixed (amount of enemies shows up correctly) download them here http://quake.speeddemosarchive.com/quake/