I am sharing kozowhs Problem.
I play stock SH3, went into AM93 (near Liverpool), found two sleeping T2, which I both torpedoed once. My crew strikes. They simply don't reload torpedoes, though no fatigue, no TC, no silent running, still torpedoes in the internal storage, automatic reload setting. All it says is "torpedo is prepared for loading" (or whatever is written in English, I use die deutsche Version, of course).
Things get even better. After the torpedo strike, a trawler and a destroyer appear, both sunk by bow torpedos. As usual, they don't reload. I saved the game, restarted it - and the torpedo tubes are filled again! No empty slot, and these filled torpedoes are even in the internal storage - as if I hadn't shot a torpedo... Great, unlimited torpedos, unlimited victims! Strangely enough, my aft torpedoes (which I used for the T2s) are still ready for loading, but don't load.
It's really a pain in the a*§%. Why don't they reload like they did the missions before.
I already encountered the problem last mission. Had all internal torps shot and tried to reload the externals. No chance. Weather was calm. No enemies near. Enough men... :hmm:
Went into Dublin to find the best hunting ground of my life there. It was like xmas. 1 DD, 2 Troop Transports, 3 Liners, 1 T3, 1 C3 and only one single Elco boat to defend the whole thing.

But I couldn't load torpedoes, so I went sight-seeing. On my way back along the coast I hit a mine, but made it back to Lorient.
Does nobody have an explanation to this?