I believe the issues that the OP states is due to the system they Klint Kubiak runs. He basically calls a play and that’s the play to be ran. There is very little in audibles to be called.
Carr is as his best when he runs the offense from the line like Drew and Peyton Manning had the freedom to do. Gruden gave him this freedom and Derek was very good in getting the offense into the correct play. This is just the OC wanting control over every aspect of the offense.