The read progression is based on the route depth and the depth chart depth for the receivers. If the QB throws a deep pass on a short pass play, there are a couple possible reasons:
1. The primary receiver is covered and the QB went to his next read progression
2. The deeper receiver was within the field of view of the QB and he decided it was a better option than the short route (mainly again due to how well the receiver was covered)
3. The randomizer for choosing the read progression gave the deeper route a greater weight than it normally would.
You can double-check the plays in question in the game log by clicking on the play name to see whether the play was a deep/medium/short pass play. If you are getting more deep pass plays called than you are expecting, be sure to look at the "View Plays" popup on your game planning screens to make sure you have enough shorter pass plays active and applicable in the given situations. The bar on that popup shows the weight that each play has. It's possible your long pass plays are getting more weight than you intend because of some other factors (such as lack of shorter pass plays or heavier weights on formations).