Here's what I've always said ...
Cowboy fans are hyper focused on the Cowboys, which is natural, and as such every missed or wrong call stirs emotions and sticks in their brains. And they are watching every down of Cowboy games, and every one of these calls or non calls has that effect.
With other game involving other teams, Cowboy fans don't focus as hard on every play so they don't see every one, they don't have the same emotional response to those missed or bad calls, and those calls don't stick in their brains every time because they just don't care as much if another team gets hurt by a call.
The result of this is that it creates the perception in the brain that it happens more often, and more egregiously with the Cowboys than with other teams.