In one scene 1980s Raphael ridicules Donny's voice. This is a pun since both characters are voiced by the same actor, Rob Paulsen.
The producers regret that they couldn't get James Avery to reprise his role as the Shredder from Teenage Mutant Ninja Turtles (1987), since he had passed away.
80s Raphael slams a pizza into a Kraang (as seen from the Kraang's point of view, he slammed it into the screen). He did this in the Teenage Mutant Ninja Turtles (1987) title sequence.
The 1980's version came under fire for potentially being too violent so the fight scenes were made intentionally tame. This is made fun of at several points throughout the episode most noticeably when Kraang is taken down using only a fire hydrant and a skipping rope.
Kraang Sub-Prime sarcastically calls himself Megan Fox. Fox was April O'Neil in Teenage Mutant Ninja Turtles (2014) and its sequels.