It's Not Easy Being Green - S5-E16
Stupidity: Unless the tow truck was someone else's or Hank had the keys surely Dale and Bill could've used it to drive Boomhauer's car back.
Is Lupin Burning... ?! - S1-E1
Stupidity: Despite the fact that there are 100 (literally) cameras around the racing circuit and (again literally) everyone from the staff to the fellow racers works for the Scorpion gang, Jigen and Lupin's switch can happen without anyone noticing, even if it involved racing side by side for a lengthy period of time.
Stupidity: The office Race is being held prisoner in has a thick wooden plank secured outside to prevent opening the door swinging to the outside, but the door was shown earlier opening to the inside. Furthermore, when Jonny rescues Race after lifting the plank, Race swings the door inside. Aside from the witch doctor guarding the shack, Race would not have been prevented from leaving.
Stupidity: An explanation is given for the reason why the bombs planted on the Gundam are not activated by remote control (they have plastic explosive in the regiment but not remote controls!), but no reason why they set the timer for the explosion to 30 minutes, way too much to be of any use in combat against the Gundam. Moreover, if the vulnerable spot of the Gundam shield were situated where it explodes at the beginning, it'd be completely useless.
Bedlam in the Big Top - S1-E10
Stupidity: The gang drives away from the circus in the Mystery Machine, and none of them notice that Scooby-Doo, a large, talking, eating-machine dog, is not with them until after they had been on the road for at least several minutes.
Stupidity: In the original, the knight of the Phoenix suddenly appeared during the arena fights interrupting the show and stealing the Gold Cloth. In this remake of the saga, Sienna/Saori Kido leaves the arena by plane during a bombardment that occurs way before Nero/Ikki arrives to steal the Cloth. There is no reason why she would fly off in her VTOL without bringing the Golden Cloth with her, then (there's a lot of time for that). Instead she leaves it for the 4 Saints for them to "protect it", against a whole army and on foot in the middle of the desert.
Stupidity: The ghosts should've noticed the money they were stealing from the US Mint hadn't got its serial numbers and Treasury seals yet.
