Continuity mistake: Simon Pegg's character shouts at Manny as he is picking up a muffin, and he slams it onto the desk, smashing it and making a large messy pile of crumbs. The shot changes, then changes back so you can see the muffin (in the same scene) and it is a perfectly formed, whole muffin with no crumbs around. Then when Fran shows up and Pegg's character leaves, the muffin is back to being a messy mound.
Continuity mistake: When Fran arrives at the store, in the shot from outside you see a pile of unopened mail on the mat just outside the door. However as Fran opens the door and walks into the shop, the pile of mail has disappeared.
Continuity mistake: When Manny is in the bath he wipes his hands dry before handling the toast, in the next shot his hands are covered in bubbles again.
Continuity mistake: In the scene where Bernard is cleaning his teeth with the floor brush, he takes a crab from the jar of water. You can see that the crab is wet from the water, but in the next shot, where you see the crab close up, it's dry.
Continuity mistake: In the scene where Bernard is trying to convince Manny he is insane, cornflakes suddenly appear stuck to Manny's dressing between shots. This is due to a short gag which was cut. (00:13:20)
Continuity mistake: Bernard's accordion in certain shots is already damaged from when he kicked it in earlier takes, and other times undamaged until he kicks it.
Continuity mistake: At the very beginning of the episode, the subtitle says, 'Bordeaux, 1900', pertaining to the origin of the grapes which would make 'a wine fit for the Holy Father himself'. When Manny picks up said bottle later in the episode, the label says, 'Appellation Bourgogne Controlée', which means the wine was made in Burgundy, and not Bordeaux.
Chosen answer: You may be thinking of S3E1, "Manny Come Home", when Manny quits and gets a job at Goliath Books next door. The device they use to scan books, look up items, or even order muffins is referred to as the "Doo-Deedee-Doo," after the sound it makes when employees scan their cards in it.