Stupidity: A major effort is put in the future to develop the time portal, so they can recruit people from the past to help fight the war in the future. Yet they never seem to think to share anything with the past about the creatures and how to kill them or find out where they came from so the can help either prevent it from happening or help save the future before humanity is wiped out. Muri does recruit Dan for this purpose but it seems wasted to only use 1 person for this much more important goal.
Stupidity: At the end of the movie there is no reason for them to start injecting toxin in the first few pods of white spikes they find, whilst they have enough explosives with them to blow the entire spaceship up without chance of waking the creatures up. They risk the creatures waking up and starting spreading over the surface 30 years earlier.