At random moments during games, I find my bullets pass right through actors, and nothing save explosives work anymore. This is permanent until I start a new game.

Is there a reason for this?

You've possibly got more than 255 Moids, or individual moving objects like legs and heads, on the map.
CC really screws up when this happens.
Press Ctrl + P when it happens, Moid count is the seventh one down.

Hit Ctrl + P and on the last line it should say 'ONE Sim Update Per Frame!'., If it doesn't say that press Ctrl + O.

Maybe...

What do you mean with that? Weapons are not firing, they turn into terrain? If it is the last one, it's probably because of the MOID thing Major pointed out.

But I'm not sure if MOPixels going through actors is related to the MOID thing, to be honest. If it was that, probably using nukes in game wouldn't work.

Are actors gibbing spontaneously?