And then I saw its a bug because there is no reason for craft just to fall. In reality it would not fall, it would go to another base.
Constantine, I can understand your frustrating with this game mechanic, but it might help to look at the logic another way. Don't think of it as the skyranger "falling" from the sky. If the aliens catch you by surprise with their base attack (and if you didn't detect it beforehand, then they did), then no one is able to send a message to warn the skyranger about the attack. So after you lose the base defense mission, the skyranger remains unaware and returns, right into an alien trap and that is why everyone is lost.
On the other hand, if you do detect the incoming alien base attack, then you can send a warning message to the skyranger before the aliens jam your communication: "Hey guys, not safe, go to another base until we give you the all clear." Then use the "airborne transfer" to divert them. Even if you don't have a free hanger, just sell another craft to make room.
So that is my thought behind this game mechanic which is true to vanilla and why I think it should stay that way. HOWEVER, what bothers me is that if you lose the base defense mission, the soldiers in transit are
deleted from the save file, rather than added to the memorial wall. This is obviously not game breaking and doesn't affect game play at all, but from a story perspective, I wish they were added to the RIP list rather than deleted.
I started a thread on this in the suggestions section, but I guess others aren't too bothered by it.