I think this is largely tied in with the fact that the only sample space we have is in fiction, which creates several reasons why the fatal flaws will occur:

  1. We do not know what aliens are like. Given that we're not even sure if there is sentient life out there, predicting their methods, appearance, and of course weaknesses is so close to impossible as to be insignificant.
  2. Fiction is written for entertainment. People will often prefer to read a story where man triumphs over the evil invaders from another planet, rather than a dismal tale of defeat by an invincible foe.
  3. Human beings are flawed. We see flaws in ourselves and those we meet every day. Since sentient life is generally imagined to act similarly to humans, they inherit things common to all of us, which includes our flaws.

So, in the end, the only real way of writing a completely realistic fiction involving aliens will be to actually come into contact with some. And, hopefully, it's only a matter of time...