Later in the war you'll have more different torpedo types to choose from and you should get used to load your torpedos manually. It's no problem at all.
The Brits turn hostile 2nd or 3rd September 1939 - if you started your patrol in August 1939 they may still be neutral right now.
You may have run into a rare undocumented bug with your torpedo status and the save game. The saves seem to be tricky for some of us while others have no problems at all.
I do save at periscope depth and it works fine, others try that and get a corrupt save that won't load again.
Try to reproduce your situation the next sortie and we may get more info about your mess.