When Bart is seen incapacitated The Silence of the Lambs (1991) style at church, he is sitting on Homer's right. But in the following scenes, he's nowhere to be found. In fact, Homer is sitting right at the end of the pulpit.
After Bart circles on his calendar his first day to go without seeing Jessica, Marge tells him it is time to go to church. But he circled a Monday, and the Simpsons go to church on Sunday.
When Bart is first seen crossing out the days in April and May on his calendar, the calendar incorrectly shows April as having 31 days and May as having only 30 days, but in the next shot of each page, the number of days is correct.
Apu can be seen in a few shots inside the Lovejoy's household after the church-goers search Jessica's room for the collection plate money. Apu is a devout Hindu and has no other reasons to be there.
Skinner pulled off the "Scothoberfest" sting on a Sunday off school grounds, so he would have no right to give Bart any sort of punishment let alone 3mths detention.
When Bart and Lisa are dressed as Native Americans, Bart positions his hand in mid-air, as if gripping an invisible shoulder, revealing the two characters had been re-positioned after being animated.