The food sack effects of Wormy Apple and Softy Kreem. The Wormy Apple decreases the food in your sack as a reference to the adage "one bad apple spoils the barrel." And why would a Softy Kreem decrease your TP? Brain Freeze, of course!
A minor one in the bonus dungeon. Remember how you needed the pickaxe item to break the walls in Tower of Druaga, but not in this game. Well, you actually are using the pickaxe from Radisrol to break the walls down!
When using the Narikiri Dolls, their effect is justified by characters switching bodies. How does one switch bodies with a dead Leon? Is the party somehow carrying his body around for this exact purpose? This shouldn't be possible, but still... *Shudder*