I'm having this problem with SoA and maybe someone of You who has the mission pack will be able to help. I'm playing on normal difficulty setting and I've reached the Mortum's Keep level. The thing is I'm at the exit and... have all secrets but only 65 of 67 possible kills. I cannot find those two remaining monsters anywhere. I've even used noclip to check the outside level boxes but didn't find anyone who wasn't teleported to the battlefield because of some bug (like the one with four scrags in the original Quake's Ebon Fortress level). There are no fishes on this level so this isn't the case (and the fish bug is fixed in SoA from what I know). Maybe the monsters should be "created" not teleported after performing certain action that i didn't? Found all the secrets, even the "Levelord giggles!" one.

Also I remember that when I played SoA years ago there was this problem of course and also another one on the Edge of Oblivion secret level. I don't remember the skill (think it was easy) that I've used to play then, but there were also one or two (can't remember exactly) monster(s) missing and nowhere to be found.
Anyone knows am I doing something wrong or is it a game issue? Quake v1.06 patched to 1.08, GLQuake v0.97.