The one big difference between the musical and the book that really irks me is the portrayal of the Marius/Eponine relationship vs the Marius/Cosette relationship. It's almost like the development of the two relationships got flipped.
Musical!Marius and Cosette get a lot of flack for being the stereotypical "love at first sight, married in days" bullcrap you see all over the place and Musical!Marius amd Eponine get to have the developed friendship that seems to go way back. It almost makes you root for Eponine over Cosette by design.
Meanwhile, Book!Marius and Cosette go through an overly-complicated courtship that lasts more than a year. They have a humorous courtship based on eye-contact for sometime before meeting in her garden several times and talking late into the night. Even before that they were vaguely aware of each other's existance and thought nothing of each other for a while. So, definitely not love at first sight, and definitely not married in days.
When I first saw the movie, I got the impression that Eponine and Marius had been childhood friends. That might have just been me, but at the very least it gives off strong impressions of a deep, long friendship. However, in the book Eponine lives next door to Marius when he first moves out. He doesn't even realize she's a girl until part way through the book, and though Eponine is head-over-heels in love with him, they barely know each other. I would call them acquaintances before I would call them friends. He doesn't even recognize her at first when she's wounded. She has to tell him who she is before he gets sad that she's dying. And it's only a little sad too. Certainly no, "A Little Fall of Rain" moment. She asks him to kiss her forehead and he's a little baffled but then again he's Marius, baffled is his key character trait.
I went into the book expecting this great backstory for the Marius/Eponine friendship and instead got a long-winded, if humorous, courtship between Marius and Cosette and I am one hundred percent okay with that. I just feel like they did us a little dirty in portraying that relationship in the musical and movie.