That's pretty funny. I mean, it sucks for those who were affected - but maybe they're trying to trixx you into playing more antagonist mode. Maybe there's a shortage of antagonists and they're trying to put you to work. This is a joke, please don't take me seriously.
Personally, I don't find it to be too world-ending, it's quite easy to earn enough stigmas to reach a high enough rank to craft. Gold is the bottleneck though, especially with the next load of raider recruits seemingly around the corner. I just wish they would give Antagonists some gold along with stigmas, or maybe a flat gold reward even if they lose the game, if they stay to the end.
Anyway, I sympathise with those affected, but try to remember that this is a small team, and they are (I assume) pushing to release the next chunk of content ASAP. A glitch in the matrix discarding your antagonist rank might seem like a simple thing to roll back, but judging by the problems they've had with the Xbox One version of the game, I don't think it's within their power to do so. Hopefully it doesn't happen again.
