As I suspected, this whole mess was somehow triggered by the Daylight Savings Time change in the US, where our servers reside. At 3AM EST, the clock changed to 4AM in the US, instantly running transfers for all players with auctions ending during that hour, including this player. While the player was affected negatively by this fact, his auction would have ended half an hour later than it did. This is nothing out of the ordinary, it happens every year when US switches and the rest of the world doesn't.
The bug that affected others a couple of hours after that was much severe and while probably triggered by the change, it definitely needed fixing and undoing the transfers that already ran.
I agree that this doesn't seem fair, so I'm open to suggestions on possible solutions.