If you look at chapter 23, there's a part where ml said he prefer alpha than omega. I believe he said it bc most of male (in this manhwa universe) will turn alpha, it's kinda rare to see male omega, that's why they all thought eunjae will be an alpha too. ML said it probably to assure eunjae that it's okay to continue the relationship even if both of them alpha.
But here's the problem, ML already said he hates omega and prefer alpha, and it turned out later on eunjae becomes omega. So eunjae thought since he turned out to be omega, it means ML will hate him. That's why in the novel later on eunjae will spend his winter break after manifesting as omega at France, then come back once new semester start, he also using drug to hide his omega traits.

I thought they were gonna break up if he became an omega not an alpha..I am confused