Their appears to be a glitch where you still here the zombies moaning in the church alter room of the matriarch of decay level after you kill them. Or am I missing something?

Also, I can not seem to find the last enemy on this level.

Also for some reason it says tragic when I activate the kill all enemies command even though I already kill the dog.

Now the the dogs corpse is gone

I haven't gotten to that level yet, but are there crucified zombies on the wall in that area? Because they don't count as enemies, but they do moan.

It's because there's one zombie that's positioned lower than the others, so if you don't gib it it gets knocked down into the floor, tries to get up for a frame, then lays down again, making it unkillable without the cheat menu.

Yeah, that's probably what happened to OP since that's exactly the enemy I was missing the first time I did that level... had to restart from to beginning since I always try to get all kills and secrets. Well, guess it was worth it at the end.