So I'm stuck at the point in the game where you're supposed to go looking for guards in the catacombs.
I found the wounded squad captain and talked to him (though he's gone now).

I found the dead guy being guarded by a spider, at the bottom of the spiral stairs, and the other guard at the top of those stairs. So that gave me two tokens, but I can not for the life of me find the third one!
Was the guard captain supposed to count as one? because if that's the case then my game bugged out and my entire save is broken.

Really hope I've just missed something obvious, because it's a fun game, but I don't want to start over.

You might not have access to the third guard yet. He's in the circular room just after the two guards, but you have to a do a few things before you can go in there.

Ah fantastic! I guess I'll have to go do some other quests then :)