In "DNA Evidence", the smoke from the office only wafts in the first few shots before Strong Bad speaks his account of what happened at Bubs' Concession Stand. After that, it disappears.
In "Strongest Man In the World", the first page reads, "Everyone loves The Homestar Runner..." instead of "Everybody loves The Homestar Runner...", which would have been the correct quotation from the original book.
In "No Hands On Deck", there is a tiny dot above Homestar's lip in the first scene when he squints his eyes and says says "I gotta level with you".
In "Quality Time", on Strong Sad's violin, the strings enter the tailpiece far too close to Strong Sad's chin. The strings of an actual violin enter near the edge of the tailpiece. Also, assuming that the gold-colored item at the end of the bow is the screw, Strong Sad is holding his bow backwards.
In "Happy Hallow-day", Strong Sad tells The Cheat, who is dressed as Gizmo from "Gremlins", that sunlight should technically turn him into a horrible beastie. In actuality, sunlight kills Mogwai instead of turning them into gremlins. It's eating after midnight that triggers the transformation.