I can justify that. MC has seen a fair share of alphas and omegas loosing their rational over pheromones since he was a kid (his alpha dad was an example), that trauma WILL leave him a scar and make him doubt whenever ML said he love MC too nonchalantly. ML may have protected MC a lot since they joined the company but MC can think it as ML was trying to score a goal to the chairman and trying to climb up in ranks. MC's pride as a rightful heir and his desparate to prove his abilities despite being an omega also covered his eyes from seeing the truth.
It was all about childhood trauma and misunderstanding but MC forgave his rapist so quick is still dumb and illogical. Poor Hyeondo has to witness his crush got treated like that and didn't even consider his plead....
the ML can rip his heart out of his chest for him and this fucker will still be like nah.