Pretty much everything that diverts from reality and is already listed under You Fail X Forever, Critical Research Error and Acceptable Breaks From Reality on TV Tropes, but especially for me how it's possible, again and again, for a puny little level one noob to grow experienced enough to take on entire armies and veterans on their own.
Sometimes it's sorta justified or averted, like NOLF2 gives you a main character with an already established badge of badassery, or Crysis 2 makes it *very* clear that what matters isn't you, it's the suit, and its regeneration abilities give you potentially infinite tries before growing more experienced. But Fable for example plays it completely straight, you're a little kid growing up in a happy-go-lucky town, then after The Call he undergoes his training and basically freelances until the plot decides to visit and eventually makes him fight a demigod (when he's most likely already reached old age).
During all this time, you're facing one villain that has the same amount of time as you to advance their skills. Apparently character development is not the only thing stagnating for villains.