Director Paul Verhoeven and Screenwriter Edward Neumeier repeatedly said in interviews that “audiences didn’t get the joke”. Here are some clues:
1. Earth’s Federation is basically a totalitarian government that limits citizen’s rights unless they serve military service. One soldier says she joined to get a special license to have children, and there are frequent references to how only citizens (those who serve the military) are the only ones with the right to vote.
2. Everybody on Earth has an unquestionable loyalty to the Federation. No crime, no rebellions, etc.
3. We are led to believe the bugs strategically attacked Earth by sending an asteroid to destroy a city. These bugs are not obviously mathematically sound, so it’s obvious they couldn’t have calculated the Earth’s position in the cosmos.
4. The use of WW2 style propaganda.
The joke is this: The bugs are totally innocent. Humans are the evil alien invaders.