It seems that nearby infantry units end up touching the main rotor of the WY-55 when they're near it, and they seem to move it around a bit.
I tested this by doing the following:
This is still present in the 1.08 main branch update.
I've noticed this happening as well, and it's pretty game-breaking when it does happen.
There is a way to remove the back seats though. Just put 'this animate ["AddBackseats",0]' in the init field of the helicopter.
You can use the animation AddBackseats to remove the rear seats, then lock those spots so units don't sit in them.
The doors and FLIR camera were neat options to be able to have on the MH-9. It seems odd to remove them unless they were causing something else to break.
I've noticed this happening as well. Something similar also happens if the vehicle is manned, it displays the respawn position as "AI: *Name of AI here*" instead of whatever's been defined as the name in the respawn module.
Just checked today's dev build. It appears to be fixed, and now lists "Hunter" or "Strider" instead of "AI: No Unit".
From some testing I've done regarding this command, it only appears to work on the "first" turret of the vehicle (Turret [0]). On vehicles with multiple "turrets" (tanks, APCs, helicopters), the command will only return magazines from the primary turret. None of the magazines from any additional turrets (commander's weapons, pilot's weapons) will be returned through this command.
Checked this today on the latest dev build. It's still an issue with the vehicle respawn module.
They're likely related, as the most likely thing that's happening with the respawn module is that it's respawning an empty UAV/UGV instead of a manned one. Can likely be fixed by using the createVehicleCrew command on the UAV/UGV when it's spawned, but I haven't tested that yet.
I've noticed this happening as well. Quite annoying when trying to play a mission with a bunch of people.