1. Chani vocal about not believing in the prophecy, highlighting a divide amongst the Fremen between those who believed in Paul as their prophesied savior and those who did not. This shit wasn't in the books, like at all. Sure, there was some skepticism that Paul was the Lisan al Gaib, but I don't remember any discussion about true believers and skeptics among the Fremen as to the prophecy itself.
2. This bugged me more than it should have: Chani's secret name being Sihaya? And hating it? My recollection from the books is that was Paul's private name for her, she was his desert spring. Maybe it was her Fremen name, too, I don't know, but it was a term of endearment between the two - she didn't hate it. And while we're discussing names, Paul did adopt the name "Muad'Dib" - he asked to specifically be called "Paul Muad'Dib."
3. Again, at the end of the movie, Chani runs off after Paul says he's going to marry Irulan. That's BS and a total bastardization of what happened in the end of the book - she sucks it up and she and Jessica bond over the knowledge that even though they were not officially married to the Atreides men, history would call them wives. And Paul never sleeps with Irulan, ever, in the sequels - only Chani, the mother of his kids.
4. Speaking of kids, Alia only appears in Paul's vision in this movie, played by starlet-of-the-moment Anya Taylor-Joy. No creepy toddler to kill Baron Harkonnen, leaving Paul to do it. And no mention of the Harkonnen raid killing Paul and Chani's baby. This also means no time-jump as occurs in the books, which means Paul's ascension to leading the Fremen happens really quickly.
5. No Guild navigators in the Emperor's entourage? Which of course simplifies the idea of Paul destroying spice production on Arrakis. But it also makes it less meaningful - there's no indication that the Guild was pulling the Emperor's strings and ignores the mechanism of spice production (and its potential destruction). And by golly, I wanted to see a Guild Navigator!
6. No Thufir Hawat in Part 2 or his suspicions that Jessica was the one who betrayed Duke Leto. Then again, no milking a cat for his antidote as in the Lynch version, either.
7. Feyd Rautha was never subjected to the gom jabbar in the books. But the final fight with Paul was excellently choreographed.
8. I couldn't buy Timothee Chalamet as leader of the Fremen. Not manly enough, which was fine for part 1 when he was still supposed to be just a 15 year old kid, but it just didn't work in part 2.
9. No funeral for Jamis? Come on! How is Usul supposed to give water to the dead when he declares himself a friend of Jamis?