The battalion who attempts to fight the Kraang are called the Earth Protection Force. This is a special military unit that appeared in the Teenage Mutant Ninja Turtles (2003) series.
In the season 2 finale, a poster advertising a screening for the documentary "Dinosaurman in NY" can be seen when Krang Prime falls to the ground. This is a reference to the Triceratons from the Mirage comics.
The Kraang shout "Exterminate!" This is the battlecry of the Daleks from the sci-fi series Doctor Who (1963). The Kraang, like the Daleks, are tentacled aliens with prominent brains and armored suits.
It is revealed in this episode that April and her dad live above an antique store named second time about. This is a reference to the 1990 live action TMNT movie
April's dad's car from his hipster days (which he aptly titled his party wagon) is a reference to original TMNT turtle van toy which was in fact a V8 Volkswagen van named the party wagon.