Just gonna list things regardless of how minor they may be.
Between the chuunin exams and the current war Rock Lee is only able to open one additional gate.
The way Rock Lee uses his bandages to magically bind an opponent is clearly not just plain taijutsu.
Obito acting like Tobi when either no one was around or when just people that already knew his identity were around is technically breaking the 4th wall since it's done solely to deceive the viewer.
Hashirama seems to be the only wood user the senju ever had historically.
Orochimaru had snake-like features well before he ever started his experiments or presumably snake-oriented training.
Tsunade's true appearance looks massively older than any of the other sannin despite them all being shown in the same starting team together under Hiruzen at roughly the same age.
When black and white zetsu separated originally at Obito's request for some reason black Zetsu despite being the entity that we now know still had a portion of white zetsu attached to him, green hair, spores, and part of that plant apparatus (all on the black zetsu side of the body mind you), despite the fact that we now know he's just a solid black, fully formed humanoid in his own right. In other words, based on the depiction, Zetsu was being portrayed as being composed of like 3/4 white zetsu.
Why does zetsu even have the plant apparatus? He doesn't have it when he's just plain white zetsu and black zetsu certainly doesn't have it on his own in his true form, so where the hell did it come from?
Neji, the highest ranking member of the original 11, and one of the most skilled, died before Tenten.
Naruto's mentor was his father's mentor, whereas Sasuke's original mentor, Kakashi, was a pupil of Naruto's father.
Edit:
In the anime, Kakashi once used the lotus, including the act of bandaging naruto's body for the drop, without having any actual bandages to use.
Madara is the only character in the series to die 3 times. Once against Hashirama, once from old age, and again at the close of the war, all while being a fully alive, living breathing person.