Badass Decay: Dairine starts off with a greater amount of power than her sister when she becomes a wizard n the third book and then falls to just above normal in the fifth. This fall is normal and expected; every wizard starts off with greater power for their initial ordeal. By the time the power drops off, their skill and knowledge increases.
Broken Base: A Wizard Abroad is a very contested book, with some fans loving the in-depth depiction of Ireland that came from Duane now living there, and others accusing it of feeling like it was written just to show off all the stuff she'd found out about the country rather than to tell an interesting story. It also doesn't help that her spellings of Irish words are very inconsistent.
So You Want to Be a Wizard: Fred worrying about a disaster like a meteor hitting Manhattan directly after Nita and Kit admire the World Trade Center. Naturally, this was taken out of the NME.
Deep Wizardry: The whole plot about stopping the East Coast from being wiped out is quite eerie after Hurricane Sandy and the 2017 hurricane season.
Two years after establishing Nita's Irish ancestry in the first book, Diane Duane met Northern Irish author Peter Morwood, who she later married, resulting in her moving to the country. This came in quite handy in letting her give an accurate portrayal of the country in A Wizard Abroad.
Dairine's manual essentially takes the form of a computer. Essentially, she's using an e-Reader.
At the start of one chapter of A Wizard Abroad, Nita discovers that Ronan is an incarnation of the One's Champion. This then goes completely unacknowledged for the rest of the chapter, not getting mentioned again until halfway through the next one. It ends up feeling a lot like Duane moved the scene back a chapter, but then didn't change anything else.
The Wizard's Dilemma keeps contriving so many reasons for Nita and Kit to not get in touch with each other that it feels more like watching Three's Company.
A Wizard Alone went through some especially heavy rewrites in the NME, thanks to the Values Dissonance of its portrayal of autism, especially the disproven notion that people with the condition don't consider anything beyond themselves "real." Unfortunately, the scene of Nita first realizing who Daryl is in her dream conversation was pretty much impossible to reconcile with this, and makes no sense at all.
Ronan and Roshaun having such similar names isn't an issue in their introductory books, but then Wizards of War suddenly puts both of them together on the same team, leading to many complaints that fans had a hard time keeping them straight.
Kit talking about Penn "throwing shade." It very much comes off as Duane desperately throwing out a slang term she doesn't really understand, to try to connect with the kids of the day.
Narm Charm: Kit and Nita taking so long to get in touch with each other during Wizard's Dilemma can feel very wearying, but looked at from the perspective of stressed and traumatized teenagers, it really hammers in how much they're going through.
The Scrappy: Carmela was very popular at first as a Badass Normal sidekick, but in Wizards at War and especially A Wizard of Mars, many fans turned on her, accusing her of having become a Creator's Pet with Duane having to do more and more ridiculous hair-splitting of the series' terminology to explain how she can do so much wizard stuff without actually being a wizard (which also has the side effect of making it seem like there's literally no upside to becoming a wizard to balance out the constant life risking on difficult assignments). Many fans also take issue with her borderline sexual harassment of Ronan and occasionally some others, saying there's no way anyone would accept this coming from a male character.
Unintentionally Unsympathetic: Roshaun was intended to at first be an unlikable character whose Hidden Depths would redeem him. Trouble is, he's such a gratuitously over the top Royal Brat throughout most of Wizard's Holiday that many fans balked at being expected to completely forgive it all just because of the reveal, especially since he never actually shows any remorse for it.
Besides dealing with various bits of Technology Marches On, the New Millenium editions also get rid of what is now seen as appalling treatment of Machu Picchu, like threatening to starve her if she doesn't give a prophecy.
The NME of A Wizard Abroad gives a more PC depiction of Irish Travelers.
In the biggest change of all, the NME of A Wizard Alone has Darryl's autism not be cured by his Ordeal, as people had started seriously frowning on real-life neurodiversity being cured by magic.
