I was in combat with Nere and disarmed him. When I picked his sword up during the fight, the deep gnomes stopped cowering and accused me of stealing, at which point they joined Nere in attacking me.

That is a good (bad) one! I'm willing to make some allowance for the underlying rules leading to odd results in some situations, given I recognise that it's not reasonable for it all to be hand-crafted. but this sounds bad enough to be considered a bug (as do some of the other examples here). Surely, the deep gnomes shouldn't care if we nick the cult's or duergar's stuff, so it sounds as though there's an issue with the way the factions in Grymforge are defined. At least it's better than the deep gnomes becoming hostile when we use AoE spells in the Nere fight as they seemed to at some point in EA, but that's a low bar
