I have never had issues with guild runs. But completely random pugs? Yes definitely. I have seen it happen to others and it's happened to me.
While I agree that often people will get upset because they didn't read the loot rules properly, I am specifically referring to cases where it's genuine ninja looting. Here is the example of what happened to me:
I had been having rotten luck getting Mirror of the Blademaster (an awesome trinket from the council boss in HFC). I wanted it especially for doing challenge modes and it just wasn't dropping, even with coins, in our guild heroic runs. So I started joining normal mode pugs to get a second chance at it.
In the third week I joined a group in which I was probably the best geared and when I joined I specifically asked if any gear was reserved. The raid leader replied that it was not. We killed the boss, the trinket dropped and my roll won. The raid leader then told me that because my gear was better (ie higher ilevel) I was inelligible for the trinket and he gave it to a hunter from his own realm (presumably his friend). When I protested he got pretty abusive and told me I should go to BRF mythic if I wanted a better trinket. Of course I reported him, and I reckon there is a good chance he got into a bit of trouble for a clear case of loot scamming, but at the end of the day I never got the reward I deserved.
Ultimately I don't care if I pugged 20 times and in those times, 95% of the items that dropped were awarded fairly or within the stated loot rules. What I remember is that one incident and it really tainted the entire pugging experience for the expansion for me.