It's stated that in the pre-screening he was supposed to be an alpha but he somehow turned into an omega and that's when the doctor asked them if he had any prolonged exposure to alpha pheromones. We've seen in the prologue that even before the secondary gender reveal ml was capable of releasing pheromones. Probably also the fact that he's part of a family full of alphas contributed to it.
That's why I jumped to that conclusion, I could be wrong tho
It may be omegaverse but some authors like to add their own spice to it.

It's not directly stated but it's pretty obvious that mc turned into an omega bc of ml's pheromones, he ruined him