The biggest problem with Moore's offense was that it featured too many option routes. Once defenses know what options will be chosen based on the coverage they show it becomes fairly simple for them to show you a coverage, let you select your routes based off it, and then shift into a different coverage at the snap, putting them in prime position to destroy your play. Better DCs figured that out and were able to neuter our offense except when we just had such superior talent that there was nothing that could be done about it even if defense knew the play.
Actually l forget I said all this.. the REAL biggest problem with Moore's offense was dude had zero feel for the running game. He would call running plays essentially as throw aways until he could get to the next pass play on his sheet. The running plays he called rarely had any real intent to them. Even when the running game is failing this season you can see they are setting things up and keeping the defense from teeing off on Dak. That's why even though the overall numbers are not great, the impact of the runs are good enough to win games.