There's been a lot of training accidents. (I think over half the deaths thus far were from training)
More than a few mis-jumps into a Star. (Calhoun, Calhoun, Calhoun again, Me, one of my attack fleet tests)
Oh, and NPC fleets near constantly flying through stars, but as they weren't loaded sectors at the time, ... (as an aside, I need to find where the Traders merchant fleet going to the Scavs hit a star, and camp there for a few days. Salvage, Salvage everywhere!)
... and then, there's the zombie Isanth brigade. -_- Every time an Isanth wave is launched, they all spawn with missing chunks.