WARNING: The following contains spoilers for Chapter 57, “Eida,” of Boruto: Naruto Next Generations by Masashi Kishimoto, Mikio Ikemoto, Mari Morimoto and Snir Aharon, now available in English from Viz Media
One of the biggest mysteries in the Boruto franchise has long been what happened to the title hero's eye at the start of the series. During the flash-forward, his right eye is scarred and seemingly missing its vision as he fights an older and much more evil Kawaki amid a destroyed Konoha. In the rubble, Kawaki makes it clear Boruto will die like Naruto and the others, which leads the Hokage's son to activate his Karma mark and a replacement eye to avenge the fallen.
While this particular duel has not been elaborated on yet, with the series focusing on him and Kawaki as brothers right now, Chapter #57 of the manga hints at a key development that could explain what happens to Boruto's eye.
In the chapter, a pensive Naruto knows Momoshiki's hold on the boy is growing. His kid could become permanently possessed by the alien warrior at some point during this arc. This causes the Hokage to admit he'll have to kill his son if things get out of hand. But when he visits Amado, the former Kara scientist reveals he has a surprise cure. Well, a temporary one, at least, that he thinks can stem the infection.
He presents Naruto with some pills, telling him they are Boruto's best chance at staving off Momoshiki's spread. He doesn't go into details about how he experimented to create the tablets, but he does hint they're from his time working under Jigen/Isshiki. There may be side effects so there's no guarantee it's the best solution, but it is better than nothing. That's why, even as Amado warns that Boruto's eyes will be in danger, or he could die, Naruto still accepts.
Unfortunately, the pills will affect his Byakugan eyes, which have been passed down from the Ōtsutsuki clan to the Hyūga, to which Hinata belongs. It's why Amado warns Naruto not to let her or their daughter, Himawari, come near the pills as they could kill them.
Given that Boruto doesn't have these eyes, his odds are better for the treatment working, but as Hinata's genes are still inside him, it's nonetheless unpredictable. Coupling that with Momoshiki having the eyes, too, and Amado really can't predict how exactly Boruto's code is being rewritten by the alien. It's a calculated risk to help the teenage shinobi, and from the info presented, it's not out of the question to infer these pills may eventually be what damage Boruto's eye.
The fact Amado mentions these specific adverse effects in the first place is a red flag. But, as he mentions how he lost a daughter, it does seem like he genuinely cares for Boruto's welfare. As such, it doesn't feel like sabotage, but even if he's a bit distrustful, a desperate Naruto has no options. He is willing to try anything at this point to protect his progeny.