Did it, though?
As you say, the first impact was on the shoulder, and that alone was going to stop him scoring. That the arm was forced toward the head (by a combination of the impact of the first contact coupled with Yaha already going to ground) is pretty incidental.
Worth noting also that the contact with the head happened with said head was about 2-3 foot from the floor, and when Makinson launched himself at Yaha, Yaha was more upright (ie, his sliding to his knees was a large factor in Makinson eventually making contact with his head)
I think it was a penalty, but nothing more