If the receiver is covered by time the QB locates him, the pass likely be broken up or intercepted.
There needs to be a double tap system where you press the button once to get the QB to look at the receiver, and a second time to throw to him. If he's covered, you don't press that button a second time and look for another option.
There needs to be somethings that indicates to the user, which receiver the QB is looking at. You could highlight the WR in some way, or have a cone.