Continuity mistake: When Lisa first discovers Jebadiah's confession, she is holding the fyffe and wearing his racoon hat, the screen fades to black (I'm guessing for the ad break) but when it comes back Lisa is standing in exactly the same position, still reading the confession, still holding the fyffe, but no longer wearing the hat.
Continuity mistake: In class, when Lisa is sitting at her desk, pondering the Jebadiah mystery, her tray of cookies and glass of milk is very visible. Then when Lisa says "The missing piece of the puzzle. I've got it." and runs out of class, the cookies and milk are no longer there.