Let me guess: are you using a IX-D2 u-boat? If so, this is a common bug. Just put in the search engine the words "IX-D2" and "bug" and you'll see plenty of topics about this issue.
I've it too, and there is nothing that can be done for it, apart:
1) do not try to transfer more than one torpedo at the same time;
2) reduce, by a small mod (don't remember its name, but you'll find it in the posts) the number of the externals;
3) exit the game and reload when the problem occurs (it is what you're doing).
I don't have this issues with other boats, apart from the IX-D2.
Hope this helps (a little).
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