The teenage winger was visibly upset when substituted by Flick during the second-half.
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Asked about Yamal's antics after the 3-0 win, Flick said: "What kind of reaction? I think it's normal.
"Look, the most important thing for me is that we played and that we have players who deserve to play, like Roony. He's a very professional player, and when he came on, he played well.
"That's what I'm focusing on."
On Marc Bernal's performance, Flick added: "Marc is a player for the future of this club and he has a great future here. I hope he stays healthy and he played a very good game. I like watching him."