Moments pages are spoilers off; beware of unmarked spoilers!
Fridge Brilliance
There are two instances where wishes are made and alternate solution suggestions are offered: Kyubey asks Michiru why she doesn't just wish her grandmother's illness away instead of simply wanting to spend one last day with her. And Michiru asks Kaoru why she doesn't wish for her own injury to be healed, rather than anyone else hurt in said soccer match to be helped. Kaoru replies that she'll return to the soccer playing field on her own merit. Both of these wishes could be seen as inverses to Mami's and Kyoko's wish.
The silhouette of the incubator making contracts with several of the magical girls in the series being different. It turns out that the Saints, upon deciding to create a system that rejects the magical-girl-to-Witch system, altered the memories of everyone in the city — including their own. The Jubey they recall when making a contract was actually Kyubey, and this explains why the incubator seen when Airi contracts is partially obscured in shadow.
The high amount of magical girls that turn into Witches in Asurano is staggeringly high, which is uncommon for the whole franchise. Then it turns out that rewriting everyone's memories and creating Jubey are a big part of this happening — with incubators being ret-gonned from everyone's memories and how Grief Seeds and Soul Gems work in conjunction, there's nothing that allows the magical girls to cleanse their Soul Gems. And while Jubey seems to be able to purify Soul Gems, he only does it for the Pleiades Saints, and then it turns out that he's not actually purifying them, but merely doing something akin to polishing the surface. The corruption and depleted magic is still there, just hidden under the surface — which is also why Niko's Soul Gem was mentioned to be completely clean when she turned into a Witch.
The formation of the Pleiades Saints is the only time a mass contract is seen in the Puella Magi franchise to date and one of the rare times where none of the girls' wishes seem to have a horrible side-effect. That's because everyone was together and had been saved by Michiru earlier. Incubators usually approach a potential magical girl when they are at their lowest, so they are more likely to make short-sighted or impulsive wishes. But since Michiru had saved everyone after they had gone past their Despair Event Horizon, and they were basically each other's support, they opted for simpler wishes — like Saki wishing for her younger sister's planted flowers to bloom forever instead of wishing her sister back to life.
On a similar note, the only one that did not openly state her wish to Kyubey was Niko, whose wish did end up badly by creating a clone that ultimately ended up a major threat to the world. Had she been open about her wish, the others could have stopped her and alter the wish.
In Niko's flashback, the children call her "Kanna", despite the flashback taking place in California. It would be rather odd for the kids to be calling their friend by her last name. We learn in Chapter 18 that they weren't - the child's first name was Kanna.
Fridge Horror
The Ultimate Madoka-created universe likely means that a lot of the series ends up being completely ret-gonned. Since magical girls no longer turn into Witches, Yuuri simply disappears after using too much magic and Airi likely never becoming a magical girl to begin with. Kazumi might not exist, period — Michiru never turned into a witch, so the Pleiades Saints had no reason to ever clone her. But since the incubators now tell the girls what happens to magical girls instead of letting them just find out, perhaps the Saints were coping better with Michiru's death.
On a semi-related note, Hijiri Kanna likely does still exist because the shooting incident in Niko's past also likely happened, and had Hijiri take over her original name and life. Just how badly was Niko's psyche likely affected by the incident, as she was willing to have a clone take over her family, friends, and future. And for that matter, where has Niko been staying while Hijiri was in her home?
On the note of the Fridge Brilliance above of Michiru and Kaoru having wishes that are inverses for Mami and Kyoko. Exactly how badly would Michiru and Kaoru had regretted their wishes, had Michiru gone against her grandmother's way of life and cured her illness or Kaoru selfishly wished to heal herself, ignoring the girl that was bullied over the injury?
Exactly how many magical girls unnecessarily turned into Witches because the barrier the Pleiades Saints had created meant they didn't know or remembered that they had to use Grief Seeds to cleanse their Soul Gems. At the very least, given the number of Soul Gems the Saints have stored in the Freezer that were about to hatch, the number is really high.
Fridge Logic
How did Yuuri and Tachibana not notice that they took the wrong trunks after bumping into each other? Kazumi and a soccer-ball-sized bomb must have quite a weight difference.
