Quoted from Oneangrymo:
I got all the way to the last mode in alien with hyperlseep multiball going on and of course something had to go wrong ! Almost all the balls got stuck in the airlock.
If you manage to send several balls into the Airlock before it kicks them out, this is possible. Shouldn't need to reset the game completely for this, though... a telescoping magnet should be able to pull them out. Where to put them afterwards is a bit of a hassle, but you could try one in the Airlock, one in the launcher lane, one in the Vent 1 saucer, and I guess throw any others in the trough. (All this because of the high power interlock that prevents you from just putting them all on a raised flipper... though perhaps you can do that if there's a nearby friend to help. The glass cartridge is a serious PITA in this situation though.)
Can you tell if the ball doesn't half enough oomph to reach the launcher lane, or if it has so much oomph that it's hitting the side wall and bouncing back into the trough? In the former case, try nudging up the power of the trough eject coil by one notch (5%); in the latter case, nudge the power down one notch.
And yes, game level and slope can affect these sorts of things too. 6.5 degrees of slope and level side-to-side is ideal.