Other mistake: Apu already knew Homer because in the flashback episode, Homer's barbershop quartet, they were in a band. However, in the scene where Homer enters the Quick-E-Mart, Apu refers to Homer as steady customer as if he didn't know him.
Character mistake: In the scene where the imposter Krusty is robbing the Kwik-e-mart, Krusty's hair is blueish green just like the real Krusty, but when Homer is describing the robber he says the the crook has red hair. This is so you have more clues on who the real impostor is. The imposter Krusty is really Sideshow-Bob who has red hair. (00:04:20 - 00:05:05)
Continuity mistake: In "Krusty Gets Busted", Krusty's natural skin colour is established as yellow. In "Brush With Greatness" we see him wiping off the clown makeup to reveal that he has yellow skin. But in "Homer's Triple Bypass", he comes to visit Homer, with his white clown face, and tells him that "this isn't make-up". Other episodes after that also show that his skin is white.
Continuity mistake: When the burglar points the gun at Apu and says "Hand over all your money in a paper bag" Apu immediately replies "Yes, yes, I will". But when Bart sees this incident on TV later, the time between the burglar demanding the money and Apu replying "Yes, yes" is much longer.
Continuity mistake: When the store is being robbed, Homer throws his bag to the side and it lands face down near the stand of chips Homer jumps into. But when they are watching the video of this incident later, the bag is standing upright, far away from the spot it previously was at.