In "Looking at a Thing in a Bag", when Bubs turns around to prepare the drinks, the shadow on his head is opposite to the shadow on his body.
In "Homestar Runner Theme Song", in the close-up of Homestar running on the Earth, the moon in front of the Earth disappears prematurely.
In "Teen Girl Squad Issue 10", near the end, in the "real life" scene, we see the "ARROWED II" paper on the desk. However, it is missing the "II".
In "Sick Day", when the scene zooms in to Homestar answering the word problem, the desk behind him disappears.
In "The Interview", Strong Bad's arms are missing during the opening rotation in the smoky office.