In the quest Righteous Retribution you have to get some bombs, blow up a ship, board another boat, then blow up a ship while on the boat. The extra action button pops up with the bombs for the first ship but when you're on the boat, the bomb action button is covered by a dismount action button.

mmm I was afraid of this. I thought it was a bad idea to put the vehicle leave button on the same as the extra action button. I think the solution to this is to split them into two modules

Unfortunately, I agree. I tried it out in a different vehicle, and I had the same problem.

This is something I'll do, I'm just at a work conference for the time being and I won't be back until early next week. So hang tight