Black Comedy Animal Cruelty: When Miwa sees Ice-Cream Kitty (as well as learning just what happened to it), she jokes that Donnie now has a guinea pig to test retro-mutagen on.
When Karai glimpses into the '87-Dimension, she thinks Lotus Blossom is her counterpart, this being a reference to Lotus Blossom being the closest to a Karai the 1987 series had.
The cat April brings with her still winds up as Ice-Cream Kitty.
While Splinter isn't a rat in this version, the cheese phone is still a thing, having been a gag-gift given to him for Father's Day.
Mirror Routine: While exploring the dimensional corridor, Mikey does this with his canon-counterpart (refered to as "2012 Mikey"). Being Mikey (both of them), they both instantly forget what was happening once they were called away.