The only specific example I remember is X2, and I'm not sure if it was ever fixed.
Both FADE and TAGES insert "triggers" in the game code that cause random problems throughout gameplay. Operation Flashpoint, TOCA Race Driver, Gothic 3 and some other European games have used such protection schemes. They always get cracked properly, however, it just takes a little longer and sometimes takes a couple of tries. You don't see this kind of protection too often, though, as it's much more of a hassle to implement than SecuRom or Safedisc.