* We know that the head ref (and probably the entire crew) was formerly from the PAC12. That means that they have been reffing Ute games for years. They're aware of the penchant for Kyle's teams to aggressively push the limits of fair play, forcing the refs to constantly throw a flag.
My assumption is that the refs don't like to be forced into it every play. I'm also assuming that the Ute coaching staff and the refs have a history of confrontation once a penalty was indeed called.
* It's been said that refs could justifiably call a holding penalty on every play, but they let most non-egregious calls go.
* My theory is that there's bad blood between the P12 refs and Whittingham. It's easy to see why that might be the case.
*Welp, a 50/50 call was made (I thought it was an egregious hold, but let's go with 50/50 for arguments sake). The call was made at just the right time to annoy Whittingham. It was still on BYU to capitalize on it, but the call itself was the equivalent of kicking sand in Kyle's face at an important juncture.
* AD Harlan gets into it because he's aware of the bad blood and he's just immature enough to lose his cool when he perceives the call to be unfair. Maybe the bad blood originates with Harlan and that's why he was on the field chirping at the ref during the final play.