Yeah. I ended up taking quite a bit of damage because of this "glitch."
I don't normally go back to a previous save, but I did this time because I thought it was completely bogus and I shouldn't have to deal with damage caused by the game's shortcoming.
Since I replayed that save, I was able to use that last torpedo. Hit a 6000 ton merchant about halfway between his bridge and his bow. Unfortunately it didn't do much damage. He didn't have any guns though, so I surfaced and started laying into him with the deck gun. I must have hit every square inch of that ship before it went down. I put well over 100 rounds right below the waterline.
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