update from enginers it looks like they noted that it wouldn’t be a hardware issue and is instead considered a visual anomaly. They mentioned that it is somewhat expected to have visual anomalies sometimes when changing applications, orientation, and folders. I just tested on my own iPhone with the stock wallpaper and it looks like it has the same issue with iOS 9.3.2 and I had never noticed it before, but it does do the ‘blink’ so to speak on the dock when its changed.