Way back when, the first time my friends and I played with Horn of Plenty, we misread it as +$1 per differently named card, not gain a card costing $1 per differently named card. We were big fans of Horn of Plenty for the first couple games until we wondered, hey, how does this thing about trashing itself work...
Most of my friends seem to overlook the discarding with Young Witch. I think they assume the paragraph text is just the Bane stuff.
Another friend felt terrible when he realized he incorrectly top-decked some Treasuries.
I've accidentally trashed some opponents' Silvers after playing Highway and a Knight. (Cost reduction in general is prone to inadvertent rules mess ups.)
I've forgotten to take my player token bonuses when playing a card (only really mattered with +1 Card).
In most of my IRL games, no one else understands lose track rules, so I have prevented some mess ups there.