Continuity mistake: When Kelly is putting the number card on Logan, you can see one on Kendall behind him, when he shouldn't have had one yet.
Continuity mistake: In "Wheels," when Artie is singing 'Dancing By Myself' and doing tricks in his wheelchair, the wheels on the back of the chair that prevent him from falling backwards disappear and reappear, depending on whether or not he is performing a trick.
Continuity mistake: Bob Fossil records Howard saying "Gorilla" on his talk box, which Howard does with a downward inflection at the end of the word. However, every time Fossil plays back Howard's "Gorilla", it has an upwards inflection at the end of the word.
Continuity mistake: During "Brand New Day", at one point, Dr. Horrible stabs a picture of Captain Hammer attached to a dartboard with a handful of darts, all right in the center of the picture. A few shots later as Dr. Horrible sits, suddenly the darts are far-more spread out. (It's in the background and can be hard to see, but it's noticeable.)
Continuity mistake: After the Squirmese chef sets up his additional ingredients, Corky answers the video phone. During Corky's conversation, Al's kitchen can be seen with no trace of the chef or his ingredients.
Continuity mistake: In the scene with the squires, right before their song, you'll see the guys laughing. There is a large, older guy sitting at a table. When you see him from the front (closer to Galavant's point of view), he's sitting about halfway down the table. But, when it shows him laughing in a close up from the other end (nearer the banner on the wall), he's sitting close to the end. This changes a lot during the scene.
Continuity mistake: When the Warners emerge from a sealed crate on Miss Flamiel's desk and start singing, Yakko instantly appears behind Wakko and Dot as soon as the shot changes.
Continuity mistake: At the diner when Tsunoda and Retsuko are talking, Tsunoda pulls out a red phone with a white heart on it from her purse. In the close up she is pulling it out with her left hand and the phone is horizontal with the heart on its side. It then cuts to a wide angle and suddenly she's holding the phone upright with both hands.