Stupidity: The plan to infiltrate Emma into the coroner's office in a body bag is stupid. She is wearing a paramedic's uniform, and we see later when Mickey arrives, nobody is checking ID papers. How would she know that there was nobody in the room when she emerged from the body bag? If she could walk about the building without being stopped, why couldn't she simply walk in through the wide open front door in the first place?
Stupidity: When Mac and Lindsay are reconstructing the stab wound found on their victim on their pig specimen, a couple of the weapons they use are long, thin knives; since they obviously don't match the circular wound, Mac at the very least would know those could be excluded by default.
The Passion of Conner - S1-E28
Stupidity: For some strange reason, Conner powered down from Triassic mode before battling Zeltrax.
Stupidity: Characters repeatedly make note of how hard to kill the Wraith are, but sometimes, especially in the final episode(s) of season 1, they go down easily in a few bullets each, and then don't even regenerate as the characters turn their attentions elsewhere.
Suggested correction: It's explained that Wraith are easier to kill the less they've fed recently, and that in later seasons, with more and more Wraith waking up, fewer and fewer are getting chances to feed before they fight the Atlantis Team.
Hanging with Axel: Part 2 - S3-E5
Stupidity: After Jaden summons Neos and Flare Scarab, he has Neos attack Axel directly. Axel uses the effect of his Firewall card to block the attack by removing a Pyro-type monster from his graveyard. After the attack is blocked, Jaden attacks directly with Flare Scarab, causing Axel to lose 1700 points because he couldn't block the attack. But if Jaden had attacked with Flare Scarab first and Neos second, Axel would have lost 2500 points from Neos' attack, instead of 1700 points from Scarab's attack. (00:08:30)
The Best Thing That Ever Could Have Happened - S5-E13
Stupidity: Eli the handyman had a heart attack on the roof where he had just finished nailing roofing nails directly into the exposed part of the shingle itself, which isn't something a real handyman would do.