!!!SPOILER!!!
You are quite right. Weikun was panicked cuz he knotted in someone which he had never done before. Knotting could've been hurt but Yeehyeon didn't feel so. Plus, Weikun was still unsure of what Yeehyeon really was. Was he really a Beta? But why the scent?
Not that Weikun was worried he might impregnated Yeehyeon, but by knotting, he's also 'transformed' Yeehyeon to an Omega bit by bit.

Sorry but... Why was he so panicked?? And what the uke mean by he understand why he panicked ?