Try playing with the settings such that you can use the external camera and then sit back so you can see the hull and where they are actually hitting. I frequently use magnetic pistols also, and have found that they'll hit the mark but still blow up or fail to detonate (with no damage). External camera is best to see what's going on, otherwise try to leave the periscope up so that the boat is still visible on the targeting scree (F6) and watch what the torpedo's are doing.
If the angle is good for magnetic and fails to pass under the keel but hits the very bottom hull section it frequently impacts but doesn't explode. It'll hit the ship and ricochete or fall dead. Can also happen if your setting is such that its maybe 0.1-0.2 meters under keel and it'll bounce off it rather than explode.
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