Wuffenloaf - S3-E1
Continuity mistake: When Joel takes the note off the door, the knife slices the paper. But in the next shot, where they're facing the camera, the note has a chunk ripped out on top.
We Let People Die Every Day - S3-E3
Continuity mistake: Joel gets himself a potato with some toppings. In the first shots you still can see the potato underneath the toppings. Right before Joel starts eating his plate is much more loaded and the potato is drowned by so much topping that you can't see the potato any more. (00:08:50 - 00:09:14)
Continuity mistake: The organ Jean is holding while talking keeps changing shape without her eating it. Sometimes the edge is jagged, has a bite out of it, or is smooth. And we usually see her holding it, and she's not twisting it around.