I've been experiencing a weird problem in my current game with ships disappearing when being towed by tugs. It's happened a couple times so far:
Gave an order to tug a space station with hangar decks and four squadrons of fighters embarked. When released, two of the squadrons had disappeared.
Just now, I disabled, boarded and captured a pair of raider ships. Gave an order to tug them back to Earth, but when the tugs reached them, they disappeared.
I haven't been able to reproduce this yet.