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.
Revealing mistake: When Charles shows the picture of the horse and says "look what you get when you search for 'Charles Boyle medal of valor'" he's typed "peanut butter the horse" into his phone.
Continuity mistake: In season 2 episode 11, Jake is shown doing at least 3 pull ups but in this episode he shows he doesn't know how to do one and Terry has to show him.
Casecation - S6-E12
Factual error: Amy is wearing a NYPD detectives badge even though she is a Sergeant at this point in the show. (00:01:00 - 00:21:20)
Your Honor - S4-E18
Continuity mistake: In the cold open, when Jake throws the door handle at the interrogation room mirror trying to break it, the handle bounces off the glass to his right, but when the shot cuts to in front of him to show his reaction, the handle flies off to his left. (00:01:00)
Casecation - S6-E12
Continuity mistake: Jake mentions that he's never wanted kids, however he has mentioned loads of times in previous seasons/episodes about wanting to become a Dad.
Other mistake: It is previously explained that Jake cannot grow a moustache, then a few seasons later Jake goes to prison and grows a moustache.
Old School - S1-E8
Visible crew/equipment: While Charles is removing the shoes you can see the reflection of a camera in the closeup shot of the suit.
Old School - S1-E8
Visible crew/equipment: While Charles is removing Scully's shoes, the reflection of a mounted camera can be seen in the close up shot of the bomb squad outfit. (00:00:01)
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 Charles gets kidnapped Terry screams out Joe instead of Charles. (00:05:50)
Continuity mistake: When Jake is explaining why he let Richmond go, the left zip of his hoodie goes from folded out to flat between shots and back again a few times. This is especially noticeable when he says "the old me." (00:18:07)
Continuity mistake: The flyers on the top and bottom of the pile Terry is holding keep changing colors.
Continuity mistake: When Jake and Boyle talk about Jake's Dad, a man (grey clothing and holding a cup) in the background (behind Boyle on the left) walks from the back to the front in the same way in both shots. (01:45:00 - 01:55:00)
Continuity mistake: When Charles is talking to Gina in the break room while wearing the mask, he takes it off. When he says she was being sweet, it's back on.
Mr. Santiago - S4-E7
Revealing mistake: When Jake is typing on his computer just before Terry talks to him about meeting Amy's dad for the first time, his computer is and remains on the desktop doing nothing. (00:02:05)
Revealing mistake: In the opening credits (the very beginning), Jake is walking and the image behind him is blurred. When it unblurs (right before it the shot changes), the phone number on the building behind him is 213 which is LA, vs. 718 which is Brooklyn.
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)
Other mistake: Holt takes the crown out of the back of Jake's cabinet. However this wouldn't be possible as the crown was in the top drawer. This would have a back on it and it wouldn't be accessible by just removing the back of the cabinet.
Other mistake: When Amy reaches down to get the key out of her shoe she literally only bends slightly. There is no way that she could've reached all the way down to her foot, or retrieve the key in the seconds before she gets it. (00:14:30)
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.