3 verses have
Yes
in Edition Clear Qur'an by Talal Itani / An-Nahl (The Bee)

16:28Those wronging their souls while the angels are taking them away—they will propose peace: “We did no wrong.” Yes you did. God is aware of what you used to do.”

16:38And they swear by God with their most solemn oaths, “God will not resurrect anyone who dies.” Yes indeed, it is a promise binding on Him, but most people do not know.

16:78God brought you out of your mothers’ wombs, not knowing anything; and He gave you the hearing, and the eyesight, and the brains; that you may give thanks.