Waiver Wire Order Messed Up- What’s the Call?

We have a keeper league, and our draft is non-snake based on prior year position as well as loser bowl. The team that wins the loser bowl is the first pick of every round, and the Super Bowl winner is 12. The winner of the loser bowl also starts off as #1 in waiver position. We had drama this week as the commissioner never set the waiver order from the beginning of the season, and #1 never noticed. He finally did this week, and notified the commissioner. The commissioner then went back and reviewed all waiver claims, and came up with the retroactive order, moving teams that had made claims to the back of the line, even though they had made claims from incorrect positions the whole season. Also, the team that had the #1 waiver spot got moved to #4, and he was pissed as he’s apparently passed on a bunch of players in order to keep the #1 spot. How do you handle something like that this late in the season?