The Harry Potter books are pretty different than the movies. This can be seen in depth over here.
My question however, is whether JK Rowling ever directly contradicted the movies with later books in ways that she hadn't before. In other words, a situation where the movies did not contradict canon up to that point, but where they did (inadvertently) contradict later book canon.
Did JK Rowling ever directly contradict the movies?
Inspired by this answer.
Yes, at least twice.
Both come from Philosopher’s Stone, which was released a year after the book version of Goblet of Fire:
In the film, after escaping from Fluffy for the first time, Ron and Harry accompany Hermione up the stairs to her dormitory (1h3m).
When they try to pull the same stunt in the book Order of the Phoenix, they discover the stairs are charmed so as to make this impossible:
“Let’s go and tell her,” said Ron. He bounded forward, pulled open the door, and set off up the spiral staircase.
He was on the sixth stair when it happened. There was a loud, wail- ing, klaxonlike sound and the steps melted together to make a long, smooth stone slide. There was a brief moment when Ron tried to keep running, arms working madly like windmills, then he toppled over backward and shot down the newly created slide, coming to rest on his back at Harry’s feet.
In the book, Harry loses consciousness before Quirrell dies.
Harry jumped to his feet, caught Quirrell by the arm and hung on as tight as he could. Quirrell screamed and tried to throw Harry off – the pain in Harry’s head was building – he couldn’t see – he could only hear Quirrell’s terrible shrieks and Voldemort’s yells of ‘KILL HIM! KILL HIM!’ and other voices, maybe in Harry’s own head, crying, ‘Harry! Harry!’
He felt Quirrell’s arm wrenched from his grasp, knew all was lost, and fell into blackness, down… down… down…
He’s conscious for Quirrell’s death in the films, which should be the trigger for him to see Thestrals in subsequent years. But he doesn’t start to see them until Order of the Phoenix, to match the timeline in the books – because Thestrals hadn’t been introduced yet.
I’m not sure this is quite cut and dried as you’d hope, but the first thing that comes to mind is Lavender Brown’s skin colour.
(In)famously, by now, Lavender Brown was a minor character in the first movies, with no lines. She was portrayed by two black actresses: Kathleen Cauley (unverified) in Chamber of Secrets and Jennifer Smith in Prisoner of Azkaban.
When the first movies were made, of course, Half-Blood Prince wasn’t out yet and the casters didn’t know that Lavender would become an important character later on. The books never actually give a proper description of Lavender, but Half-Blood Prince does have the following quote:
Harry looked into the corner she was indicating. There, in full view of the whole room, stood Ron wrapped so closely around Lavender Brown it was hard to tell whose hands were whose.
While this could just be hyperbole, it at least implies that Lavender is white. If she were black (at least if she were as dark in skin tone as Kathleen Cauley and Jennifer Smith are), there would be absolutely no trouble telling her and Ron’s hands apart, regardless of how closely wrapped around each other they were.
This isn't quite what you're looking for. But the latter part of your question ("The movies said something which didn't contradict canon at the time, but Rowling subsequently wrote something to contradict it") makes me think of the problem of the Thestrals.
At the time the Harry Potter and the Philosopher's Stone film came out, Order of the Phoenix had yet to be written. A minor plot point from that book is that there are creatures flying around Hogwarts that only those who have seen death can see. Harry sees them for the first time after seeing Cedric Diggory die at the end of the previous book.
But in the films, Harry sees (causes, really) the death of Professor Quirrell, which he's unconscious for in the books. This leads to a plot hole in the movies, where Harry suddenly sees Thestrals he's supposed to have been seeing for the past four years.
Again, not quite what you're looking for, but an interesting case of the filmmakers writing themselves into a corner because they didn't know what was going to be in future books.
