There was a strange bug affecting double elimination tournaments with qualifying matches. Under some circumstances after qualifying match scores were reported, first round matches would appear to get mixed up (labels would no longer be in alphabetical order). This would result in winners advancing to unexpected positions in the bracket. Fortunately, matches on the back end were fine, so the patch just applied retroactively fixes any affected brackets. Unfortunately, many people may have already run from Challonge in terror.
Thanks to those who pointed this out!