First year, cut bait. If it were a long standing league I might have a little latitude such as an e-mail/post stating we need to review this for next year, but once games have been played it is not really an option to retroactively fix it. Complete d move to delete the post, but just another reason I would cut bait.
Similar situation in our league (which has been together 24 years) and it turned out in my favor in retrospect - but it was still foul. Playoff seeding is division winners get top 3 seeds and remaining seeds are determined by overall record, then division record, then head to head, then point differential (points scored minus points against). Once seeds set, one bracket was 1v8 and 4v5; other bracket was 2 v 7 and 3 v 6.
Well commish's buddy was the 3 seed and l was the 2. 6 and 7 seeds had identical records overall and division, split head to head, and point differential in head to head AND overall favored Team B. However when commish manually set the playoffs he had Team A at 6 seed and Team B at 7 seed. Mind you Team B was projected to score some ridiculously low amount in Playoff round 1 due to injuries and matchups so it was very obvious the commish was setting the bracket to favor his buddy. Before the first round game, I pointed out the error in seeding and was told his reasoning was his buddy's team played a tougher schedule so deserved the higher seed (mind you not following the established rules for seeding). So I left it with we need to revisit this next year so there is no subjectivity in seeding - follow the formula and don't arbitrarily "award" seeds. Well, fantasy being what it is the team I wound up playing had a terrible week and the team I was supposed to be playing would have beat me (projected terrible, but wound up scoring 3rd highest total of the week), but instead lost to the the commish's buddy (who scored 2nd highest of the week). Round two rolls around and I knock off the commish's buddy (who would have beaten the guy he beat the week before who he shoudl have played this week but was now in the consolation bracket instead of having advanced if he would have beat me).
Commish comes back and states he wants to correct the error heading into finals - it should be his buddy in the finals when all corrections made. Fortunately he, his buddy and the guy who lost round 1 were the only votes saying the correction should be made, the rest of the league voted to play out the playoffs as he had bracketed them. So now I wind up in the finals in a tainted manner, but I was the one who called out the error prior to playoff week 1 and was shot down by the commish. The only guy I feel bad for is the guy who should have beat me in Round 1, who would have lost last week but got screwed by the arbitrary seeding. In the end had the commish just followed the rules, his buddy would be in the finals - but by trying to manipulate the seedings to his buddies advantage it cost him a shot at the championship.