I thought the first 30 minutes (approx) had plenty of "supposed to be funny" moments in it that weren't.
I'm not sure why the bad guy pretty much killed the inexplicably-hotly-dressed female who helped him escape, or how she had a spare bug that apparently only this species creates when he is the last of that species, or how after all the soldiers float off into space, he manages to hop out of the same hole, remain on the edge of the building where the hole is as if gravity is constant with Earth on the moon, then start moon-hopping. Or how someone talks in a vacuum.
There were a couple of bits that made me laugh, then the plot continued and concluded in the most predictable fashion possible, then agent K is all happy even though history for him ought to have followed exactly the same course as it did when he was apparently miserable (or 'not easy to make happy' or however you perceive his character change to be).
The goody alien was just one big annoying plot device. He may as well have been a suitcase that appeared out of thin air with the movie script in and the arcnet device.