The short answer to the question of why alien mortal enemies of humanity always have some fatal flaw is that most common of statistical errors: the self-selected sample group.
Now for the long answer.
Granted the demonstrable fact that Earth has not, as of yet, actually been invaded by an otherworldly menace theoretically capable of conquering the planet, we are free to conclude that all extraterrestrial invasions are taking place in either
- A future timeline
- A possible future
- An inevitable future
- A parallel universe
Therefore since we have not actually been invaded yet, we have no personal, first-hand experience and must instead rely entirely on accounts we receive from such alternate realities.
Now that we have established our sources, we must consider them as reliable or unreliable, and also as a representative sample group or a non-representative sample group. Only if our sources are both reliable and representative of the whole can we make such absolute statements as "always" or "every" when considering our mortal enemies vís-a-vís fatal flaws.
Reliability
The question assumes that our sources are reliable, that is, that all alternate realties we have heard from are accurately representing the results of their alien invasions. We cannot ascertain the accuracy of these statements without evidence, but our only evidence is the statements themselves. But why would they lie? One possibility is that they are being forced to give false statements by the aliens who have, indeed, conquered them and wish to put us off our guard with false information. The reliability cannot be checked, and there is a possible motive for false information. Any stories we hear urging us to trade our nuclear missiles in for the alien's one weakness, delicious candy, should be viewed with suspicion. Therefore: the information cannot be regarded as reliable.
Representative Sample Group
There are two possible results of an invasion by the mortal enemies of humanity.
Alternate Earths which have been invaded and survived:
This is the alternate Earth we assume when asking the question. These Earths have been invaded, discovered the invader's fatal flaw, exploited it, and survived. These Earths are likely giving us advance warning so we can identify the fatal flaws in our universe's analogous alien invaders.
Alternate Earths which have been invaded and were conquered:
Should an alternate Earth be invaded and conquered, we would likely hear nothing at all from them, or possibly even propaganda they were forced to deliver by their new alien overlords (see reliability, above). Much less likely, but still possible, are the warnings of a small but plucky group of freedom fighters which survives in isolated pockets of resistance, giving us advance warning before it is too late. This is the idea behind the Terminator series, although these mortal enemies of humanity are, in fact, terrestrial and beyond the scope of this article.
Conclusion
So we see that the stories we have heard of alien invasions are both unreliable and non-representative, and we cannot make such blanket statements as "alien mortal enemies of humanity always have some fatal flaw". Any stories of alternate Earths which have been invaded by mortal enemies of humanity without fatal flaws would be extremely unlikely to reach us, least of all with anything resembling reliable accuracy.