While Milhouse and Lisa are inside the torture chamber, climbing up the spikes like a ladder, you can clearly see blue sky in the distance but in the next scene Milhouse head pops out of the top of the closed pyramid.
Homer and Marge are using leaves to cover themselves before eating the apple, in the biblical story only after eating the apple Adam and Eve realize they are naked which results in them using the leaves for cover.
Homer and Marge, as Adam and Eve, have belly buttons. Since they are created by God in this segment, and were not born naturally from a woman's body, they should not have them.
In the Moses segment, Wiggum asks Moses "Where's your messiah now?" The concept of a Jewish messiah did not exist when Moses was alive.