Adaptation Displacement: It's an "adaptation" of a Japanese novel that it's actually more of a loosely-connected sequel to. Notably, the author of the original work loved this movie and said that it was perfect as a "unique sequel."
Crowning Music of Awesome: "Kawaranai Mono" by Hanako Oku—played when Makoto realizes she has one time leap left and knows she can help Chiaki. She rushes out of her house and makes three leaps as she heads back in time while seeing memories of when Kousuke and she first met Chiaki and developed their friendship.
Disproportionate Retribution: The classmate Makoto causes to have a cookery accident in her place blames her for it and the consequent bullying he experiences (which admittedly was fairly extreme) to the point that he snaps, turns a fire extinguisher on her and when that fails, throws it bodily at her.
Idiot Plot: Makoto would never have had the bike crash if she'd bothered to test her brakes for one instant, or tried anything other than flying down a very steep hill packed with people and with a railway crossing at the bottom at full speed. A competent cyclist would have started braking, if only lightly, the moment the hill began and would have had plenty of time to get off the thing. Made worse when the same thing happens to the supposedly-responsible Kosuke later.
The plot also depends on Chiaki losing the time travel device he needs to get home and never asking Makoto about it even when he suspects she's leaping.
Shocking Swerve: Well, to several viewers/reviewers at any rate, the last forty minutes were just slightly out of left field. Up until that point, it followed pretty much every convention of a girl's coming-of-age anime, until Chiaki reveals he's from the future. When you're expecting the typically-unexplained magic power that ends in a lesson about responsibility and with status quo being God, it's a bit unexpected.
Rewatch Bonus: First time you watch the film this is true, but if you watch the film again, there are hints and subtle foreshadowing that Chiaki knows about time traveling, you just don't pick up on them first time round.
Values Dissonance: A number of Japanese reviewers on Amazon HATE Makoto for swapping in her classmate in home ec and making him the target of bullies, thereby probably dooming him for life. And not even feeling sorry for it or trying to change it (although presumably it is undone along with all of her other changes during the final time leap). This point, along with her eliminating her friend's relationship with Chiaki, is almost never brought up by Western audiences.
Because Chiaki steps in front of Makoto to shield her from an incoming fire extingusher and gets injured, Makoto uses a time leap to push him out of the way. However, this time around it's Yuri who gets injured.