Boruto: Naruto Next Generations is the sequel to Masashi Kishimoto's Naruto series with Boruto Uzumaki, Naruto's son, as the protagonist. Boruto is set years after the conclusion of the Fourth Great Ninja War in an era of peace where Naruto Uzumaki is the Seventh Hokage of Konohagakure.
Although the times have moved on, the need for ninjas still remains. At the same time, several massive powers threaten the ninja world. Although Boruto is, more or less, a decent continuation of the original series, some aspects of the story simply don't make much sense.
9 Boruto Vs Momoshiki
Boruto Uzumaki, being the protagonist of the Boruto series, was one of the main characters in the fight against Momoshiki Otsutsuki. Although Naruto Uzumaki and Sasuke did the major part and nearly defeated Momoshiki, it was Boruto who, in the end, finished him off.
That in itself is quite questionable, given that Boruto is barely as strong as a Chunin at this point in the anime. What's even more confusing is how Boruto was momentarily able to match Momoshiki Otsutsuki in combat.
8 Isshiki Otsutsuki's Existence
Following the death of Momoshiki Otsutsuki, Isshiki stepped up and became the main villain in the Boruto series. He was revealed to have been the partner of Kaguya Otsutsuki long ago and together, the two planned to harvest a chakra fruit on earth.
Sadly for Isshiki, Kaguya had other plans and turned on him. Isshiki survived a near-death encounter and took control of Jigen's body. He tried to find a suitable vessel, however, didn't find one until Kawaki, which doesn't make much sense given he had hundreds of years to look for one.
7 Naruto And Sasuke's Powers
Boruto: Naruto Next Generations is the story of Boruto Uzumaki and there's no doubt that he has to take the center stage most of the time. However, that certainly shouldn't mean that to make Boruto look better, characters such as Naruto Uzumaki and Sasuke Uchiha have to be nerfed.
Sadly, that is exactly what seems to be happening with the story, and most of their fights end with them being weakened in some way. Naruto and Sasuke barely use the maximum potential of the powers they possess and lose most battles.
6 Kara's Existence
Kara is a criminal organization in the Boruto world that was created by Jigen with the goal to harvest the God Tree and gain more power. Once again, the existence of the organization doesn't make much sense as Jigen has been Isshiki's host for over 500 years.
For Kara to somehow exist now, fans have to wonder what Jigen was doing for all the centuries that he had at his disposal to craft a better plan.
5 Kaguya Otsutsuki's Origin
In the original Naruto series, it was revealed that Kaguya Otsutsuki came to earth all alone and then ate the chakra fruit of the God Tree at one point. Using her godly powers, she then ended all wars and ruled as the Rabbit Goddess.
Kaguya's story was changed quite a bit in Boruto as she arrived with Isshiki Otsutsuki and decided to betray the clan for some reason. In fact, Kaguya was revealed to be the lower-ranked Otsutsuki and weaker than Isshiki.
4 The Origin Of Chakra
The Naruto series told fans that chakra didn't always exist on earth. It belonged to Kaguya Otsutsuki, who received it after eating the chakra fruit of the God Tree. After having two children, Kaguya Otsutsuki's chakra was also shared with her sons.
In the coming years, Hagoromo Otsutsuki, Kaguya's son, traveled across the world and spread chakra using ninshu, and eventually, it was distributed to everyone. In Boruto, chakra was already on Earth when Kaguya and Isshiki arrived, which is quite confusing as it shouldn't have existed in the first place.
3 The Ten-Tails
The Ten-Tails is another major aspect of the story that doesn't make much sense in Boruto. According to the story that Hagoromo Otsutsuki told fans, the Ten-Tails was the beastly form of Kaguya Otsutsuki when she combined her powers with that of the God Tree to reclaim her chakra.
In Boruto, however, the Ten-Tails was revealed to be a seed that every Otsutsuki carries with them. By planting a Ten-Tails seed, a God Tree emerges and eventually bears a chakra fruit.
2 Ao's Survival
The Fourth Great Ninja War in Naruto saw countless ninjas fall; one of its biggest casualties was Ao, a sensor-type ninja from Kirigakure. Ao was the head of the Sensor Division during the Fourth Great Ninja War and was thus situated in the HQ. Unfortunately, Ao, along with the others there, became a target for the wrath of the Ten-Tails and was thought to have died. Surprisingly, in Boruto, Ao is revealed to be alive, which doesn't make sense as the Ten-Tails' hit them head-on with power great enough to destroy countries.
1 Kashin Koji's Existence
In Boruto, Kashin Koji is a scientifically created artificial human who serves Kara, an evil organization. Right from the very beginning, some big question marks were raised about Kashin Koji's motivations.
Eventually, it was revealed that Koji was a clone of Jiraiya. Once again, this doesn't make much sense as Amado would've needed his DNA to make a clone and according to Kabuto Yakushi, attaining his DNA for Edo Tensei was impossible.
