There was never a time when they didn't like each other - Minato (Omega) and Jin (Alpha) have sworn ...
Omega made questionable choices. Even though he’s in love w his alpha childhood friend, he decided to sell his body and slept w random men after he finds out that he has a very low fertility rate even for an omega. The alpha comes from a powerful family that’s in need of an heir, so he selfishly decided that they shouldn’t be together because he can’t reproduce and therefore is worthless. Not once did he consult with the alpha or at least try to make a baby with him. And once he DOES get the miracle pregnancy, he decided to hide himself and the child forever because NOW he’s ashamed of his past for sleeping around, thinking he’s now too dirty to be with the alpha. Meanwhile, it changed nothing, the alpha left his family anyways to be with the omega, before he even knew the omega got pregnant
Basically the omega was selfish from beginning until the end. If he had made different choices he wouldn’t have slept w random men, they could’ve been together as intended from the start, and alpha would’ve still inherited the family.