Revealing mistake: During "Brand New Day", watch the background as Dr. Horrible appears as a giant and stomps down the city-street. As he takes his first step, a piece of concrete from building to his right falls off and hits the ground. However, if you look closely, it's obviously a quickly-made computer effect. As the piece of concrete hits the ground, it simply vanishes, and is replaced by a rather odd-looking animated "poof" of dust. The issue is the concrete piece was much bigger than the cloud of dust, so it's clear that the piece simply disappears right as the dust-poof appears.
Revealing mistake: During "A Man's Gotta Do", when Captain Hammer kneels down and crushes the gizmo on top of the van, you can briefly catch a glimpse of a black safety cable next to his knee.