Well what also doesn’t help is the fact he’s the reason Juhyeok is a omega, his pheromones were scenting him when they were younger as the doctor explained so it can cause slight resentment, and when he found out Juhyeok is a omega he thought since he’s a alpha they both can be together, now Su-ah would probably be happy if he was the omega and Juhyeok the alpha but what if he wasn’t and they were both alpha that’s probably Juhyeok mindset

See this is how I understood the story so far.
First they're both wrong and hurting themselves.
Juhyeok since they are young have been protective of Su-ah because when they were young he was timid. So juhyeok work extra hard to strengthen himself because he promised Su-ah to always protect him or that's what he wanted, and everyone in their circle believes so as well. Then when he presented as Omega suddenly everyone is treating him like a weak person like the stereotype Omega (fragile and needs to be protected), and of course I understand the side of his mom too she just doesn't know. But anyways, so when Juhyeok is hurting about this fact and not because he presented as Omega, even when they went to college he was treated as nothing but an Omega even though he is part of the Judo or Taekwondo team. And he doesn't hate Su-ah or being with him it's just that whenever they're together he can't seem to control his pheromones whenever Su-ah is around and didn't know at first that Su-ah was coating him with his Alpha pheromones which Juhyeok didn't want (which is understandable), but I think it's also because Juhyeok wants to show Su-ah that he's the same person as they were young the one that can protect him and take care of himself, he wants Su-ah to realize that he is not the stereotype Omega.
Su-ah really loves juhyeok we can see that since they were young is a real sweet child and loves how juhyeok cares and protects him. Then he presented as Alpha he thinks that as an Alpha Juhyeok would not like him or would stop being protective of him as the stereotype to be Alpha should be the stronger and protective one, so the solution he came up with was covering juhyeok with his pheromones so juhyeok will be dependent to him (which is totally wrong in my opinion) but as he see Juhyeok strengthening himself and always pushing him away he doesn't even want him going to his gym. he thinks juhyeok is rejecting him because he became Alpha. And I also think he wants to prove to Juhyeok the he as an Alpha that can protect them both and he really wants to show to Juhyeok how much he loves him by being there always.
This is how I understood the story so far and I think what they need is a slumber party just talking to each other how they feel after getting they're secondary genders because that's where it all went downhill...
Please don't be mad at me this is 100% my opinion I just want to share