Do you have the SHIII Commander "Malfunctions - Sabotage" feature activated?
Engine trouble is a common malfunction.
Though I'm sure it's realistic I turned that feature off myself. Felt like about every patrol there was something wrong with this or that.
I may go back to switching it on every few patrols, or even every so it's still a part of the game just not so frequent.
Anyway, that may not be it. Just a suggestion.
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