When we see God he has five fingers for the majority of the episode, but in the last scene, where Homer questions the meaning of life, God only has four fingers.
When Flanders rescues Homer from the fire at his house, there isn't much snow on the ground. The very next shot, there is snow completely covering the ground. Most of it disappears another scene later.
The hairs in Homer's combover are shown burning off in the fire but in the next shot they're back.
Maggie turns her bottle upside down in the cold church and a frozen cylinder of ice slides out. The bottle clearly tapers to the nipple end, so the ice block would remain in place.
Ned Flanders rescues Homer from the fire in his house while everyone is at church. But Ned being the fanatical Christian that he is, would also have been at church.
Santa's Little Helper steals Homer's chocolate bar as he was evacuating the house on fire, even though chocolate is bad for dogs.