Stupidity: Lance and Lana's actions at the end don't make sense, other than to set up conflict for the plot. Lance won't give Lana a shot. Lana steals a vile and after Lance injects Lex (to stop him, fine), he finds Lana, who is trying to inject herself. He stops her, throws her back, then proceeds to try and inject her. He could have just waited and let her do it herself, or taken the vile and left. Lana is then scared that Lance is about to inject her when that's what she wanted in the first place.
Day 4: 11:00 P.M.-12:00 A.M. - S4-E17
Stupidity: When the couple is in the plant they call Jack on the cellphone, he instructs them to open the case and separate the book from the activation device. This was stupid, he should have told them to destroy it, since the codes had changed the moment Air Force One crashed, and it would take about 1 hour to make this work. This is explained later on in the show.
Stupidity: The last remaining Xindi, in desperation, attempts to release the virus over the fan, despite the virus not being fully ready. However, it seems the only reason he didn't release the virus at that time was he had to seek cover from Archer and T'Pol shooting at him and to start shooting back at them. However, he had plenty of cover from the rooftop stairwell, which was right next to the fan, and he had enough time to dump out the contents over the fan.