I noticed two things that don't seem right with boarding shuttles:
When you launch a boarding party at an enemy and the shuttles are still on their way they get bugged if you switch target. As soon as you target another enemy (which happens quite often, since boarding parties are most efficient against larger ships that deploy mines or fighters) the shuttles drift lethargically in space and do nothing anymore. Forever - except they get shot down. Which is quite annoying since the Boarding Party skill has quite a cooldown, and you wasted it for nothing in that case.
When you launch boarding shuttles at an enemy, and that enemy is destroyed before they reach him, they just drift along in space and wait for you to leave system or get shot. This is not as bad as my first concern, but I think they should at least return to your ship or "beam" back. Those shuttles drifting in space and doing nothing are annoying.