Need help clearing up rule :

the playoff rule for 24 team leagues is as follows

...

24-team leagues - Semi-Finals:
The 4 winners of the Quarter-Finals matchups advance to the Semi-Finals. They will be re-seeded by win-loss record, with all Wild Card teams always seeded below all Division Winners. The Semi-Finals matchups will be Seed 1 vs. Seed 4, and Seed 2 vs. Seed 3. The better Seed has home-field advantage in each series.

it simply states:

Wild Card teams always seeded below all Division Winners.!!!!!!!!!!!!!!!!!!!!!!!

Under my theory, the Wild Card Surfer Dudes team is still the fourth seed. What changed is who the number one seed is. If you take the first round of the playoffs into account The Long Run has the best win loss record (by a tiny margin) and becomes the first seed for the second round. Again I don't know if this is what actually what happened, but it explains the seeding and is actually consistent with the text.

As it turns out, it was a bug in the software. Strat tech support did not answer over the weekend but they have updated the software now. They were unwilling or unable to dial back the semi-finals' games that were played, however they did give a credit to each of the 4 teams that were impacted by the error.