I'd be willing to bet one of the issues of their offensive operation is the verbiage with their play calls. It's one of the drawbacks of the West Coast Offense, because some plays have a tag for damn near every position on the field. Russell may be having a hard time adjusting to that part, depending on how intricate the playcalls were in Seattle.
The Jets used to have very similar issues with their offensive operation when Hackett's dad (Paul) was the OC under Herm Edwards, particularly whenever Vinny Testaverde was starting. Once Chad Pennington was inserted, the operation ran smoother. By the time Paul Hackett became OC, Vinny was a long time NFL QB playing in the WCO for the first time. By the time Nathaniel Hackett became the Broncos HC, Russell Wilson was a long time NFL QB who I'm assuming is playing in the WCO for the first time, so it makes you wonder if something similar is occurring in regards to Vinny & Russ not being comfortable yet with the verbiage aspect of the playcalling.
Regardless, it's still a coaching issue and it needs to be cleaned up, whatever it is. I'm not trying to pass the buck from Hackett to Wilson, just throwing out some food for thought about Denver's shoddy coordination.
And if anyone knows for sure, please correct me if I'm incorrect about this being Wilson's first time running the WCO. I can't remember if Pete Caroll ever hired an OC that ran it during Wilson's time in Seattle.