Character mistake: When Wunch frisks Holt in order to "check for a wire," she appears to forget that her actions are easily visible through the interrogation room's mirror, something a high ranking official in the NYPD would not likely forget. (00:11:41)
Character mistake: Captain Holt calls the Pimento case "Operation 225641441636324" which he said he arrived by placing a numerical value to each letter in Pimento and then squaring it. But the perfect squares couldn't match up to Pimento since there's only 6 perfect squares and Pimento has 7 letters (plus the last 2 perfect squares don't fit the pattern of the previous 4). Nor is "225641441636324" a perfect square.
Character mistake: When Charles is talking about Terry's kids you can see Stephanie Beatriz (Rosa) trying not to completely crack up next to him.
Character mistake: When Gina tries to set up Rosa on a date, Rosa mentions the last person Gina set her up with (Justin) was a dork who rode a Yamaha motorcycle. She says "he might as well have picked me up in a station wagon." Rosa's bike is a Yamaha R1.
Character mistake: When Charles gets kidnapped Terry screams out Joe instead of Charles. (00:05:50)
Character mistake: Jake and Rosa are looking around in The Apartment for months. 14 CIS workers are analyzing The Apartment. All of them are looking for a killer who never left The Apartment. Still, in multiple months no-one thinks about checking the person-sized vents. Seems pretty unlikely. Vents are literally the first thing anybody thinks about when people try to disappear. And a vent of this size is a dead giveaway that someone for sure would have checked.
Answer: In reality, the Commissioner is a civilian administrator, appointed by the mayor of New York City. He (as of this writing, the role has always been filled by a man; the show gets that part right) is usually someone who has risen through the ranks of the NYPD, but upon becoming Commissioner, is no longer a sworn member of the force (the highest sworn rank is that of Chief). Since Commissioners are appointed, technically anyone can serve in the position, including Deputy Commissioners (who are appointed, in turn, by the Commissioner himself).
Update: On 1 January 2022, Keechant Sewell became the first ever female commissioner of the NYPD.