The turtles somehow have money, Michaelangelo is broke and decides to get a job. There is no way the turtles can work without being recognized. This fact is pointed out to him seconds later, which is why he dons the disguise to apply at the pizza parlor.
In season 1 the star cruiser the Neutrinos left to the Turtles was blue, but here it's red. It's entirely possible they painted it red while fixing it up.
When the Rat King comes out of the sewer, the mailbox behind him is misspelled "US MALE".
(Possibly deliberate) Donatello the smartest turtle doesn't seem to recognize Shredder's voice on the phone. It goes with this episode's running gag of the turtles seeing or hearing parts of Shredder and thinking they seem familiar.