I had a similar event in one of my games: a planet with a colony of mine disappeared completely (no asteroid field left, no log message). It was a random event because when I replayed the turn it didn't occur again.
Try to replay your savegame again to see if it happens always or just randomly.
When I reported this here on the forum some beta-testers confirmed they had seen something similar as a rare event.
Just see it as an undocumented event of the game: there are strange things happening in the universe!
