Yuka thinks Kaoru is an Omega, and we get the story from his pov, but I'm pretty sure Kaoru is actually an Alpha.
In my theory (which would make the most sense for a manga), Kaoru is flustered because he's feeling Yuka's pheromones strongly, since Yuka is his mate. As an Alpha, it's difficult to resist to the pull, especially when it's his mate, so he starts avoiding Yuka : he doesn't want to loose control (like the other alpha did) and inadvertently hurt Yuka or force him in any way.
You can see at the end of the chapter that Kaoru became flustered again when Yuka started getting in heat, and tries to stop the other alpha even in his state. The other alpha doesn't react to him the way an alpha would react to an omega in heat, so it makes the thoery even more realistic.
If I've got it right, next chapter they'll clash other Yuka and Kaoru will reveal to Yuka that he is an alpha. Note that Kaoru being an omega was never confirmed, only imagined by Yuka who's judging based on Kaoru's quiet and unconfrontational nature.
Whaoo, I just wrote a dictionary xD
I love this !!! Kaoru is obviously an alpha and yuka's mate, which is why he gets flustered around yuka and tried to avoid him. He doesn't want to jump on his friend who he's treasured since childhood even if yuka was a bit of a prick xD
Btw, is it just me or are there suddenly a ton of omegaverse stories ? I remember searching for one a while back and there wasn't any, but now every week at least there's a new one