During the ending cutscene, when Sly and Carmelita are discussing music, a pink record of Neil Diamond Live can be seen next to Carmelita's chair. This could be a subtle joke on the fact that Neil Diamond made a song called "Carmelita's Eyes."
During the cutscene after Spoiler:Neyla joins herself with the Clockwerk frame and becomes Clock-La, there appears to be a glitch with the model used for the boss. What is supposed to be either yellow eyes that glow red or completely red eyes, has one eye turned red and the other yellow with red.
At the end of the crypt in episode five "A Tangled Web", using the Binocucom whilst standing on a pillar, you can see Jojo the Raccoon hovering above the coffin, the main antagonist from Sucker Punch's first game "Rocket: Robot of Wheels".
In the fifth episode "A Tangled Web", in the graveyard are gravestones which read "RIP Rocket". This is a reference to the character Rocket from the Nintendo 64 game "Rocket: Robot on Wheels", Sucker Punch's first game.
There is a level that was left out of the game. It would have taken place in Monaco and have a mission where Bentley steals a yacht, smashes it into the docks, and rams it into the casino. It is unknown why it was left out.
If you hold down R1, R2, L1 and L2 at the title screen in Ratch & Clank: Up Your Arsenal, a hidden demo of Sly 2: Band of Thieves will be unlocked. Successfully completing the demo will give you access to a cheat which replaces your wrench with a double-bladed laser sword.