funny how these aliens have all this power to travel across the galaxy and technology far far beyond what we have today, yet Jeff Goldblum was able to plant a virus on the "mother ship" with an old laptop and was able take them all down thanks to a ship that crash landed on earth 20-years ago and even more amazing how the aliens didn't notice it was an old/retired ship.
everything is always just perfect in movies.
Or you could use an explanation that is improbable. You know, just like some events in real human history.

Jeff was a super genius savant, and that is why he cracked the signal and determined it was cycling down in the first place. Hell, he even figured out what their plan was.
As to the issues with the ship and uploading the virus: Perhaps the aliens suffer from hubris and incompetence even more than we do. Since their tech is organic in nature, maybe they are basically an idiocracy. So, when shit goes bad, they have no ability to alter strategy and tactics. The established invasion doctrine could have been in place for 1000 of years, and they merely follow it. Or it could be genetic like real locusts. Once Jeff jury rigged a way to interface with their tech, it could have been a completely unsecured environment. So everything connected is vulnerable to malicious code.
I can keep going. But, the whole point is to suspend disbelief and roll with it. If you have to critically evaluate everything you watch, then your idea of fun ain't mine.