The flashback to Gina asking if anyone else gets a "gay vibe" form Captain Holt does not match the footage from when she initially asked.
When Jake is holding up the picture of the murder victim at the deli, in the reverse shots he is holding it by the bottom right corner but in the forward shots he is holding it along the bottom edge, closer to the left corner.
Captain McGinley is wearing several citation bars that are not issued by the NYPD. Also, NYPD regulations require that the American Flag bar be worn as the highest citation bar, McGinley wears the American Flag as his lowest bar.
When Terry is pointing out people in the squad to Captain Holt, you see Scully and Hitchcock with a female middle-aged detective, Daniels, and they are introduced as a group. After this point Daniels is never seen again, and Scully and Hitchcock are instead seen as partners.
Captain Holt has a black WTC commendation on his badge. That commendation bar, awarded to any officer who was on duty or responded on September 11, 2001, is worn higher than any other award or commendation, except for the American Flag bar.
In the opening scene, Jake says they are looking for "three white males, one of whom has tat sleeves on both arms," yet in the footage all three men are wearing jackets covering their arms.
When Peralta, Santiago, and Captain Holt are running from the car Jake is putting his vest on incorrectly: he has his head through the arm hole.
When Amy asks Jake what he's doing, he tells her he's doing the speech from Donnie Brasco, then corrects himself and says that 10 of him are doing the speech from Donnie Brasco. There are 11 TVs visible behind him showing his image, so that's at least 11 of him doing the speech (12 if you count the real him in addition to the television images).
Amy tells Holt and Jake that Ratko isn't listed in the self-storage ledger, so he must have used cash. Even if he paid cash, his name would still be in the records as the renter of a unit, there just wouldn't be a credit card or checking account on file. She likely meant he must have used an alias, though given that Peralto had established that Ratko was a made up name in the previous scene, that would have been a given.