Character mistake: During the last class trial (06), Kyoko recapping the vitals of the victim gets them wrong, saying she was 5'6" instead of the correct 5'7" as written everywhere else. Nobody corrects her (and the exact vitals are an important part of the trial, and the mistake happens exactly when they come into play). A wrong number slipped in the script.
Other mistake: In chapter one, when Sayaka Maizono comes to the protagonist's room and tells him in the React question; "Just a little while ago, I was lying down in my room...And all of a sudden, my door started rattling and shaking", the text is labeled wrongly as being spoken by Makoto Naegi instead.
Other mistake: In Chapter 3, when Jiro is found in the pool, the narration says "Without a missing a bit, Hina started putting on the Robo Justice costume." Bit for "beat", obviously.
Other mistake: In Chapter 3, the kids find the computer with Alter Ego. The text says the computer screen glows "a pale green", but the artwork shows a unequivocally blue hue.
Other mistake: In the first class trial, the narration says "The air seemed to grow heavy as we sat there", with a picture of all the protagonists standing in a circle.
Other mistake: In chapter 2, the protagonist wakes up at 7am with the announcement and goes to check out Mondo and Taka as fast as he can. He meets them, and Aoi says "They've been like this all morning", but it's just a few mins past 7 and the cafeteria where all the captive kids have to gather has just opened.
Other mistake: The first event that lets you befriend him contains the line "Mondo and I went to the dining hall", with a fade to black. One of the very few possible times to have Free time with Mondo can be triggered in the Dining Hall in chapter 2, so you 'go' where you already are.
Revealing mistake: In the presentation for the fellow Ultimate Students, the screen scrolls showing several magazines Junko, the Ultimate Fashionista, has appeared in. In the background, one of the magazines has obvious jibberish filler text in it, since it goes, I quote: "argrwgawrg agreg agregraegraaerg asg."