Mr. Burns mentions that mutants have been created by the Nuclear Power Plant "Everybody knows our mutants have flippers".
Homer Simpson got arrested for not paying for parking tickets resulted from previous episode " City of New York vs Homer Simpson".
The scene in Judge Snyder's courtroom where Lisa is put on trial for stealing the skeleton is seen as a reference to the 1920s Scopes Monkey Trial in Dayton, Tennessee, which dealt with issues of separation of church and state and the debate between creationism and evolutionism.
The publicity stunt created by the mall developers in the episode has been compared to scientific hoaxes such as the Cardiff Giant and the Piltdown Man.
At the end of the episode, when Lisa asks if the townspeople are outraged for being fooled by a publicity stunt, Chief Wiggum is about to answer her, but is distracted when he catches sight of a Pottery Barn in the new Heavenly Hills mall.
The students digging by the sunset and their silhouettes are shown is similar to the scene in Raiders of the Lost Ark when Indiana Jones and Sallah free the Egyptian excavators from the Nazis, and they in turn help Indy. The scene against the sun is when Sallah tells Indy that the workers have found the Well of Souls.
Lisa was arrested for destroying the angel, however she is only 8, therefore she would be below the age of criminal responsibility in almost every state.
While the angel supporters are wrecking the museum, Moe is crushed by a mammoth tusk and claims to be paralyzed. In the very next shot, Moe can be seen in the mob heading toward the laboratory.
When everyone goes to the Heaven Hills Mall it is completely dark, however it was merely minutes after sunset.
During the scene where all the Springfield residents head to the Heaven Hills Mall, Maggie's bow is missing.