No you can't load them into the boat as a pair. Drag one then the other to the internal spares slots.

When you can't get them in, the only thing other than what's been mentioned could be injured crew. Doubtful that's the cause but check by talking to the crew you can. It will show in the upper right of the box in red if they are injured.

Other than that, i don't see why...:-?

But what mods are you using? It can be a corrupted one :yep:

I think this is just a bug that is in the stock game with one of the u-boats. Im sure also that it will fix itself when you reboot the game and/or dock/end patrol:hmmm:

Remember also. You can't transfer the aft external torpedo to the forward internal slots or vice versa ( forward external to the aft internal slot). I tried and it wont work because they are facing in opposite directions.