Ah - this is something of a bug, but it's a tricky one to fix, and given that its impact is generally low, it's a low-priority one. I can't honestly see taking the time for this (and it would unfortunately take a fair bit of time) over doing something else more high-value unless somehow this became a big issue for something in vanilla.
... which, of course, leaves you in a lurch with what you're doing - my apologies!
(Judging from your screenshot, btw, it looks like you might have shields inside the bounds of the hull? If that's correct, that could cause other collision-related problems as well.)