When Sideshow Bob is shocked by Marge his hair goes up into a big round Afro like the one he had in his first appearance in TheTelltaleHead.
When Homer and Sideshow Bob enter the Kwik-E Mart, Bob remembers that he robbed the mart while dressed like Krusty in Krusty Gets Busted only to be foiled by Bart. Apu even remembers Bob's robbery. Homer was also there when it happened but he doesn't mention it.
Sideshow Bob shot himself out of a cannon during the parade, which was also a reference to him being shot as Krusty's sidekick in Krusty Gets Busted.
In the scene where Homer and Bob are chasing Frank Grimes Jr. in the FXX version, you can see his cape fall off. Then you see Homer and Bob again. But when you see FG Jr. again, he is still wearing his cape. Then, when he turns into the alley his cape is gone again.
After Moe's pickle jar gets shot, there is a shot that goes to the wall and slowly looks at each picture. When we first see it, there are six pictures shown. Two larger ones on the right side, and four smaller pictures vertically down the left side. The picture in question is the large one in the bottom right corner. Originally, it is Moe in Egypt with the jar, and then when they do all the close up pictures, it suddenly changes to a picture of Moe and his jar laying on the beach.
After Bob stabs Bart's pajamas with the knife, his stomach is visible, but when you see Bart looking at his watch, it isn't visible, but when you see Bart again, you can see it again.