This is a really bizarre effect that is only reproducible in MP. This doesn't occur in SP.
If you put the bone stock 'armed speedboat' or any mod thereof into MP and shoot it, it will frequently fail to completely die.
It may partially disappear though.
Sometimes you'll be left with only the wake traveling around, shooting at you. Other times, the crew will be gone from the boat, which will still be there shooting at you.
But it absolutely cannot be fully killed. Screenshots of bizzarity included. Let me know if I can provide further information in any way.