Q: If someone plays Beam Us Up, and the Transporter/Teleporter is in play, but it’s Malfunctioning, would that player still get all of the Crew/Beings in play?

A: If your Transporter is Malfunctioning, no, it will not get you all the Crew in play. You will get the same effect from Beam Us Up as if you had no Transporter.

(Note that in Star Fluxx, it’s called a Teleporter, and the Keepers which are Beamed Up are Beings, not Crew, but this question could still arise if Beam Us Up is played with a Malfunctioning Teleporter)