Without question these.

Fruit flies.

Submarines are massive, and made to withstand the huge force of pressure that acts on the hull at depth. No animal can externally cause damage. These little assholes on the other hand can cause turmoil.

Prior to sailing you will fill the submarine with food. Tinned, frozen and whatever fresh you can, including sacks and sacks of potatoes. Somewhere in those sacks of spuds, there are probably some fruit flies, just waiting to get onboard and start reproducing.

So you shut the hatches and dive with a couple of families of fruit flies, abundant food and 180 odd sailors unaware of the coming swarm.

Once they start breeding, you can’t avoid them. They are everywhere, and you spend the next couple of months looking forward to finishing the fresh food so you can try and clean out the store rooms.

An animal isn’t going to damage a submarine, but millions of tiny ones inside will drive their crew wild.