He knew how they looked at each other was too intimate for them to be just good friends.
There was no reason to Arthur be bothered with this fact. He was a liberal person, after all. If one of his knights decided to fall in love with his manservant it was a private matter of them.
But inexplicably was not how things worked.
Gwaine reach more than 3 feet away from Merlin made him feel uncomfortable. The jokes he did not understand, the same effect. Was he... jealous?
No! What a stupid thing to think about. He was happy with Gwen and had everything we wanted to have.
(Everything except what he really wanted. And he had not courage enough to fight to get.)