Mika's chair is missing. Seia's little bird isn't there. Nagisa is on her phone despite it being a tea party session. None of them seem to have weapon holsters. The emblem patch on Mika's uniform is not the Trinity logo but instead a whole different thing that only vaguely resembles the Trinity logo.
The Abydos logo on the tags are extremely simplified. Some are saying animation error, but I doubt it as other illustrations such as the restaurant logo and the background adverts have full detail. Also Hosh seems weirdly energetic as well.

The fake FSC logo has an almond flower, consistent with the almond theme of this story volume. Also there seems to be an "irregularity meter" below the Jeremiah 1:11 thing. Maybe the skibidi toilet guy wants the irregularity meter to be at 1, so whatever is left of the real Kivotos is erased?

Makoto wouldn't look at Ibuki like that, knowing how much she adores her.

Other things that are notably missing that I and others may or may have not mentioned already include RABBIT Squad, the animal and robot NPCs, Kronos news reporting (replaced by a generic news bulletin with an adult-looking reporter), and more importantly, guns (apart from FOX Squad's), and
any trace of the previous FSC president.