Plot hole: The whole team went into the match, and the tournament, without knowing its rules. They all are totally surprised by the fact that the top 2 teams qualify from each group. Of course, that's quite impossible, especially since there are veterans in the team, Tsubasa is a football fanatic, Misaki is a clever student of the game, and you just don't walk into a tournament you have prepared for and looked forward to for ages without knowing such a basic fact.
Plot hole: Once Wakabayashi wins his challenge against the Nankatsu senior students, he instantly is back at his huge mansion to collect Tsubasa's message. Tsubasa was standing just a few meters away watching The Challenge as it happened, and Genzo had no reason to run away (if anything he was supposed to supervise the team during training), nor he's shown doing that. He's just gone, no explanation. (00:15:20)