I bought for the first time the apple Sonya from Hein’s apple stand in La Crescent, MN. I noted that one apple had an area of green that was about the size of a dime on the top of the apple. I hypothesized the spot did not turn red due a leaf covering this area? Thoughts?

See this web site. Possibly a mild sunburn spot? 
https://apps.extension.umn.edu/garden/diagnose/plant/fruit/apple/fruitspots/fruitsbs.html

I bought for the first time the apple Sonya from Hein’s apple stand in La Crescent, MN. I noted that one apple had an area of green that was about the size of a dime on the top of the apple. I hypothesized the spot did not turn red due a leaf covering this area? Thoughts?

See this web site. Sorry, I forgot what color the spot was. Your theory is more likely.
https://apps.extension.umn.edu/garden/diagnose/plant/fruit/apple/fruitspots/fruitsbs.html