It is their obvious bias that provides fans with doubt and distrust.
I have several irritations with officials. There is always the fear that the fans are influencing the calls, and many officials add to that suspicion when they exaggerate their calls that might be taken well by the home fans. It's like they are trying to curry favor with the fans.
Some officials get on some conference page to make specific types of calls, which they do to excess. Then, as the game or season wears on, we are back to where we were. Often, we see specific calls made out front, whereas the official underneath the basket is making different calls. It gets the players confused as to what to expect.
My real pet peeve is officials who call what they think happened or what they think is expected. To a large extent, this began most flagrantly in pro basketball as the league decided it needed superstars. A superstar could do no wrong. It got so bad that it probably, almost certainly, defined championships. I don't know why they thought they needed stars in order to market the game, but it led to some of the most absurd bias in sports. For a while, I couldn't tell the difference between pro wrestling.
One of the primary beneficiaries was Jordan. I once saw Jordan drive the lane and miss a layup because he was just showing off, rather lethargically. They called a foul on the drive. There were no defenders in the lane or near the lane. It was a wide open drive. Nobody even stuck out a hand to come within three or four feet of him. He just blew a layup. He sank both free throws, and I turned off pro basketball. It was enough, and it happened too often. Jordan wasn't the only beneficiary. But, he was the most flagrant that I saw.
In college ball, it seems that officials are more likely to give someone a call because of their reputation. One player has a reputation for being great. So, you let their fouls go, whereas you call fouls on someone guarding them. It's not trying to market something like in pro basketball. It's more like an insecurity. Everyone says this person is great so I have to go along with it.
The failure of an official to sit Mulkey down isn't really a problem with officials. If someone did that, the conference would likely get rid of them. Baylor has enough pull to defend an insult to their queen. They could actually make calls that would limit her effectiveness, like calling technicals when she has people make certain fouls deliberately knowing that they will not be called, i.e., fouling Courtney while she is out of bounds.
It is obvious that the charging/blocking calls have become a nightmare for officials. I really can't help with that one based on how the rules are written. Too many mistakes are made on this call. But, the call that I think is rarely called enough is the bar arm that players use to push off an opponent as they drive. That is a charge, and it is rarely called.
I will make a suggestion to officials. If you have called more than forty fouls in a game, it should require a report as to what one team or the other was doing with fouls in order to gain a strategical advantage. We shouldn't live at the line, and our bench players should not be in the game with two minutes gone.