The goof items below may give away important plot points.
Just before the commercial break, Chuck realizes Pigby accidentally pushed Sister Larue off the tower when Pigby does the same thing to her. The narrator states "it was a secret she would take to the grave." But after the commercial break, Olive rescues Chuck and Chuck tells her immediately.
In the flashback near the end detailing how Sister Larue died, there is already bat poop on the priest's back before they fight - it's there as he approaches her to talk, gone when she throws him into her lab table, and back again just before he gets slammed against the wall.