Yeah i found a small solution which was to sell the plane (while it was chasing the ship) just DO NOT touch the plane button. it will stay in the earth screen for a while like a month i think then it just dissapeard.
I always have a Skyranger with crew at my first 3 bases. I make sure i can get every UFO that Preferably lands
ahh well finished it again now. Maybe i will go complete Fallout... again.