I'd say the most critical is the back row bug, actually all bugs relating to the weapon bits. They're never unset, so if you equip a long range weapon that character will always have a long range attack. The only weapon bit that I know is unset properly is metallic.
There's also the no-critical hit property that doesn't get unset.
The immune property gives 99% evasion.
I don't call it a bug.. given that the Glass Hat/Helmet isn't worth a damn otherwise... though it makes the Adamant Armor insanely more powerful than intended.
Then there's the Immune Property+Elemental Bug where removing equipment with said property will then be weak vs the elementals.
There's the monsters don't react to Reflected spells bug.. where counters are not executed.
Also, there's the Stop+Sleep/Paralysis/Gradual Petrification bug.
Oh, there's the obvious Sylph costs no MP bug.
There are probably a few others I can't think off the top of my head.