For me the biggest issue is that the 'what if I'm wrong?' question that comes up on big/important decisions.
If you make a bad call against Arsenal it's going to be huge story in the press for ages, you'll probably get taken off games, etc.
If you make the same call against Bournemouth it's a footnote to the story and nothing much happens.
That means the threshold to give a red card for a clear 2nd booking is higher for some than it is for others and that's the inconsistency that we all hate.
On top of that you then also have the club/player reputation. Newcastle right now have a reputation for being aggressive which means refs go into their games knowing there's going to be challenges that the opposition will be upset about and that fore-knowledge sits there and has the ref thinking that if he's too card happy he'll lose control so he lets a few go and it means they keep kicking people until he eventually reaches for a card. This is exactly why Hughes got away with his clear yellow on McGinn the other night.
Forest and Wolves seem to have decided that they were going to try to 'solve' this by whining and, given it has worked to a degreee I can see us starting to follow their lead a little. We've definitely been a little more willing to call things out since Man U one.
The squeaky wheel always gets the grease