I feel like the rules are somewhat arbitrary on this point. On the one hand, if you're throwing a right hook and the guy turns and your punch lands on the back of his head, that's part of the game and no one's going to argue it. But if they're on the ground against the cage and you try to knee them in the body and hit their head instead, there's at least going to be a pause in the action, and maybe it'll even be a DQ (or at least a NC).
In this particular instance, I'm fine with the move not being illegal, but I wouldn't have an issue with them stopping the fight and giving the guy on the bottom his five minutes. No one's trying to kick someone in the cup, but the ref will still pause the fight if it happens. Same situation here.
