In "Narrator", during the Lugnut and Squeak scene, the Battleship images on the playing boards are slightly disproportionate when the camera zooms in on Strong Bad.
In "Senior Prom", when the scene is focused on Strong Sad and Coach Z, it can be seen that the table is on the blue mat. However in the following far shot, it is on the wood.
At the end of "Death Metal", when Strong Bad stands up, his legs are an abnormal gray color. As he walks away they, fluctuate independently between gray and the usual black.
In "Boring (Really)", Bubs looks unusually shorter and smaller than Strong Bad when the former walks up to Homestar and Strong Bad.
In "Technology", when Strong Bad turns his head when saying "magic" and "pants right now!", it appears his face and the chalkboard are together, because his mask is the same color as the chalkboard.
In "Retirement", right after Strong Bad deletes the email on the Tandy 400 and is about to impale the keyboard with a pickax, for a split second, you can hear Homestar saying "deleted", but his mouth doesn't appear to move.
In email #100 ("Flashback"), Strong Bad claims to have lost count of the number of emails checked at #51 ("Website"). But in email #136 ("Geddup Noise"), he makes a reference to email #84 ("Kids' Book"), in which, he claims, was around the time when the Geddup Noise gained popularity. A shot of that email is even seen in the background during this part.
In "Redesign", when Coach Z walks in front of the green screen, the edge of the carpet can be seen through his ankles. This should not happen, as Coach Z's feet would fully block the view of the carpet whether the green-replacement effect has "removed" Coach Z's feet or not.