There's no doubt that Hermione Granger is one of the best characters in Harry Potter. She's incredibly smart, brave, capable, and the Chosen One himself would clearly be dead several times over without her in his corner. For young girls, Hermione is a role model - but that doesn't mean that she is perfect, unfortunately.
In fact, in many ways, Hermione got worse and worse as the book and film series continued. The little girl with frizzy hair certainly improved in other ways, and watching her grow up and grow into her strengths was amazing... but these are some ways that she actually went downhill over time.
Lost Control Of Her Temper
Hermione is not the kind of girl who really cares about fitting in, or who just wants to sit back and go unnoticed... at least, she isn't by the end, and that's not a bad thing. The awkward girl of the first book who ran away to cry in the toilets about being disliked isn't exactly what anyone wants for Hermione, but she actually took her transformation too far. She went from mousy to fiery - and then over the top, to the point that she was actually a bit violent at times. She punches Malfoy, she sets a flock of tiny birds on Ron... really, she should have learned to control her temper, not just give into it.
Became Angry At Other's Success
Hermione started off as a total know it all, and thankfully that got toned down, but she became increasingly upset when other people did better than her, which isn't that much better. When Harry was using the Half-Blood Prince's book in potions, Hermione was frazzled and furious - not really because of cheating, but because she hated seeing her own best friend succeed where she wasn't. That's not a good look on anyone.
Went From Refusing To Cheat... To Helping Ron & Harry Cheat
Speaking of cheating... While it was a positive thing to see Hermione loosen her death grip on the rules and learn to relax a little, in some ways she took it too far. In the books, Hermione is seen to be taking over Ron and Harry's homework on what seems like a regular basis - and while she may sigh and cluck while doing it, is it really a good thing for her to start taking over for them? Perhaps if she let them do their own learning, they wouldn't rely on her quite so much.
Turned Into A Magic Snob
Similar to her increasing jealous of her friends' talents, Hermione becomes increasingly snobby about any magic that she, personally, is not good at - and it's not a good look for her to grow into.
Divination is a big one, which Hermione stomps out of when she's not immediately talented, declaring the whole thing to be not real magic... despite the fact that it's certainly 'real' enough to be taught at school, and every fan knows how real prophecies can be. This doesn't feel like a legitimate dismissal of a class, but a temper tantrum because she can't handle not being the best.
Turned In An Overall Snob
For someone who deals with the stigma of being muggle-born, Hermione certainly turns into a bit of a snob as she grows up - especially when it comes to other women. She's dismissive of Luna, seeing the quirky Ravenclaw as 'weird' and therefore not good enough for her and her friends. She looks down on the Patil twins for their love of Divination, and makes snippy comments to or about most of the other young women in her own House, too.
She Got Jealous
ittedly, this may be a reasonable part of growing up and starting to have feelings for boys, but Hermione definitely wasn't her best self during the time that Ron and Lavender were together. She was rude and mean toward Ron's girlfriend, dismissive and rude to Ron, and put Harry in the middle of it all. She even got violent in her jealousy, with that bird attack. Understandable for a teen girl, maybe. But a way that the character improved? Hardly.
Vanity
ittedly, this may also be something of a natural and common part of growing up, but still. Hermione initially didn't really care about her appearance, but became increasingly concerned with it as time went on. She got the nurse to magically shrink her teeth, and used a straightening potion on her hair.
It's far from the worst thing, and she definitely wasn't overly concerned about her looks when hunting Horcruxes, but it wasn't the best development for her.
Stopped Confiding in Ron and Harry
For a while there, Hermione actually seemed to be opening up to her friends... but by the end, she was far more like her old self, hiding things and convinced her plan was right. She didn't tell them about packing her beaded bag, she kept secrets when they were hunting for Horcruxes (and that was part of what drove Ron away), and while she was sometimes open, she was increasingly secretive about too many things - even just the little things, like staying in touch with Krum.
SPEW
Like many things, this didn't make it from the books into the films, but Hermione's 'charitable' efforts in SPEW were not a positive move for her. Having learned about House Elves, Hermione was appalled - but instead of doing what she would on any other subject and researching and talking to the House Elves themselves (and learning that they were very happy), she decided to crusade on their behalf. Even when it made them upset and uncomfortable, she pushed past - still that know it all kid who couldn't listen. Having otherwise seemed to move past the Mrs Right part of her personality, this felt like a step backwards.
Settling With Ron
It's no secret that this was something that bothered many fans - Hermione, in the end, settles down and marries Ron, despite the fact that he is objectively terrible for her. Getting together as teens is understandable, but also frustrating (because the need for a romantic subplot seems contrived and like a disservice to Hermione's ability to stand on her own). But staying that way for the rest of her life, just to fulfill the need for female character to get married and settle down? This was an area where Hermione deserved so much more.