A couple of examples then.
Having a close-knit guild we ran with a priority-based (main>off, raider>trial) roll system for loot with people often agreeing to pass for the greatest need. This worked well, but the nature of the rng and loot tables meant that some people had dry spells from time to time. One raider who was a long-time member got frustrated with this. A key part of managing this person’s concerns was to PM him an extract of the EQDKP table for the guild listing drops per person, usually showing him on par with the others of his class. We never used the DKP scores, and never made the existence of the site public, but we still gathered and held the information so that if someone raised concerns we could check their validity and reassure them if needed. It was very tempting to write this person off as a “lootwhore”, but people have short memories and so returning to the facts helped in this case.
The other example concerns a member who was hugely indignant about being accused of ninjaing blues in a PuG. This one didn’t turn out very well, partly because of language issues, but when one of our officers approached the raider about the issue the phrase he kept using was “I don’t care if you did it or not, you just need to apologise”. Exactly your early point, to the player the key issue was that they didn’t believe they’d done anything wrong, while the officer was looking at how to get a resolution. After this, we quickly pushed out a “quick guide to dispute resolution” to the officers, which seemed to help a bit.

A general point about the generation of guild nerdrage is that leaders and officers often forget that members do not get to see officer chat or officer forums, so if you’re not transparent enough it can appear that nothing’s being done about the concerns of the membership. Moving from founding officer to member recently has definitely brought that home to me.