SH3 Commander offers malfunction or sabotage options.
Second option are mines.
Third one is that you are running the GW 24h Fatique Model and there are issues with some boats. Could you PLZ tell us if you installed the 24h mod and what boat did you use.
For the "!" signs. They mean fatigue. Didn't you ever notice them before in vanilla (or was your first play with GW?
). Crew efficiency goes doen if they are too tired!