WARNING: The following contains spoilers for the Boruto anime, streaming now on Crunchyroll, and Sasuke Shinden: The Teacher's Star Pupil by Jun Esaka and Masashi Kishimoto, available in English from Viz Media now.
In the Naruto franchise, Orochimaru was one of the series' most demented villains. He defected from Konoha, worked with the Akatsuki, and ultimately, was a pawn of Obito and Madara Uchiha as they unleashed Kaguya on the world.
Most notably, Orochimaru strongly believed in science, using various experiments to power his body up while also wanting to use certain ninjas as vessels. Thankfully, he redeemed himself and helped Naruto's alliance takedown Kaguya's forces, but while in the Boruto series, Orochimaru as a scientist who no longer threatens the world, he has shown potential to revert to his sly ways.
One major red flag comes in the Sasuke Shinden: The Teacher's Star Pupil novel, where Mitsuki reveals Team 7 has been training with Sasuke. In Naruto: Shippuden, Orochimaru was obsessed with the Uchiha clan, especially Sasuke and Itachi, and numerous times, he tried to use cursed seals so he could place his essence in their bodies. He believes they were the perfect ninjas, and it's why he tried to tempt Sasuke with Team Taka -- soldiers that he experimented on offered up as war puppets as part of a bribe. He also failed to place snake bite on Itachi, who'd later burn a possession tool out of Sasuke's body that Orochimaru planted like a vampire.
So, when Orochimaru hears Sasuke's their mentor and suddenly becomes interested, that's not a good thing. He queries how Sasuke, still on probation after being a villain himself, is back from Ranger duty -- and Mitsuki finds it a bit awkward. We're not sure if he knows Orochimaru's full history with the brothers but the fact his dad is so alarmed raises his suspicions. Seeing as Mitsuki is his clone, and the interest Orochimaru's taking by periodically updating the kid's body from time to time, he could program Mitsuki to someday place a seal on Sasuke or his daughter, Sarada, to complete the research started years ago. After all, they trust Mitsuki and Orochimaru is able to alter the kid's memories, so there's potential to make him a sleeper agent.
This issue also rears its head in the current arc of the Boruto anime where Mitsuki has been damaged badly after Deepa, Kara's Joker, cut loose and beat up Team 7. He now has to regenerate Mitsuki's organs after the young shinobi went into Sage Mode to save his friends, and the older clone, Log, is monitoring what's happening closely. He knows Orochimaru has sentimental attachment to Mitsuki but it could be more due to Mitsuki being a project than his son.
Seeing as Orochimaru has experimented with Hashirama's (the first Hokage) DNA, there's always a chance he can relapse. His work also led to his protege, Kabuto, augmenting to become a snake monster too, so now that no one's keeping tabs on him, there could be other experiments being run. He's never made it a secret that he can create a new Mitsuki, so there is a constant window for creating a more sinister copy of the kid to infiltrate Konoha. Either way, we expect Sasuke and Orochimaru to meet soon to discuss the past, and only then will we know the snake ninja's true intentions, and if he's really atoning.
