Does this happen when you are also shooting an air gun or a 22 rifle? I'm guessing not near as bad.

What we call that in the trap shootin game is the common flinch. One of the main reasons that a person gets into flinchin is he or she is subconsciously antisapating the bang or hit on the shoulder or cheek. You simply raise your head or blink or close your eye at the pull of the trigger. My guess is all the above. A lot of times this is created by shooting to heavy of a load.

The only suggestion I know to offer is go to the lightest load you can, make yourself stay into the gun an keep your eye open till you see the target hit. If necessary, start by mastering this with a 22.

A lighter trigger pull will also make a huge difference. You may even want to consider trading into a double trigger ML.