When your agent is in the rubber dinghy don't panic when you hear the horrendous crunching noise should that dinghy bump into your submarine.
The devs overlooked the fact that the sound file for the dinghy bumping into something is the same sound file for a ship colliding with the sub. A horrendous oversight IMHO but we're stuck with it. That being said, it's just a minor immersion killer and only happens IF the rubber boat bumps into your sub. It does NOT cause damage.
I tried a couple of years ago to change that sound effect for the rubber boat (I found a sound file of a canoe hitting a dock, very soft 'bump' sound) but unfortunately it made the sound of ship collision the same (i.e. a soft 'bump' sound), kinda ridiculous but funny. Needless to say, I changed it back.
I'm not aware of any modder who addressed this. I don't think it can be done as I think the sound file for that particular action is hard-coded so to speak.