When the boys are in the Hardly Boys house, Stan is on the right side of the screen, yet when the government enters the house Stan is still on the right side of the screen, despite them having turned around to face the government. Indicated by the two statues behind Stan and Kyle.
Mr. Mackey comes on the intercom and says that Clyde couldn't possibly have been the one that defecated in the urinal because he had a colostomy at age five. Yet in Marjorine (2005), after the boys steal the future-telling device from the girls' slumber party, when Clyde strips off his clothes and is showered off he has no physical sign of a colostomy (i.e. stoma in the abdomen).
Stan and Kyle change places multiple times when confronting the supposedly dead site runner in the alleyway.
When the Hardly Boys are hired to investigate "The Case of the World Trade Center Conspiracy," Frank says that his "clue" is pointing to the left, yet he turns to point it to the audience's left, which is his own right.