After all the plot points Kishimoto did over the years, the very first chapter became filled with problematic instances:
- How come there's at least one orphanage in the Land of Fire but neither Naruto nor Sasuke were sent there?
- How come he was so lonely in academy if Chouji, Shikamaru and Kiba befriended him?
- How come the Uzumaki were so intimately related to Konoha but nobody joined the pieces when it came to Naruto?
- How come nobody looked at Naruto and thought of Minato when he's the spitting image of his father?
But if we were to fish all the plot holes and other silly instances, we'd probably come up with an entire page of them.