3 of them that is... poor Elizabeth, an expert in hand to hand combat AND ship based weapons, apparently was not included in that beam out. She was in the same room, but still pounding away at the blast door to the cockpit to escape the firefight.
I sent the transporter room chief on the next boarding action. To an AI ship. That'll teach him.

So I don't know if this is working as intended. I think as long as it is the same room, they should be beamed out, regardless of what action they're undertaking, be it breaching a door, engaging in hand-to-hand combat, pew-pewing a dude, or humping the system icon trying to break it.
Another thing I've noticed, which I don't know if it's working as intended either: when enemy ships cloak, my weapons stop charging. Seems wonky, as why would they stop powering up? I have not been able to tell if it works in reverse (I cloak, enemy weapons don't charge). Was that done for game balance to help the AI out?
Otherwise, a hella fun game. I've been playing non-stop since I installed it. I'm never going to get to my backlog of Steam games now
