Well, there's Precocious Apprentice, which up until now was a topic of debate for early PrC entry. Some say it contradicts itself and is really poorly worded.
Also, what about the Dead condition as being poorly defined too?
Another one: damage based on weight(wth) and carrying capacity exppnentially strength-dependent, which leads to hulking hurlers literally throwing the whole ground/mountain/planet.
Lastly, just ranting on Setting Sun's Hydra Slaying Strike, although it's more of false advertising than borkenness.