Visible crew/equipment: In the beginning where Amanda Waller is talking in a restaurant. While the camera focuses on her towards the end of the scene, they move the camera right, facing towards her left side of her face. Watch the wine glass, you'll see the crew moving along with the camera.
Deliberate mistake: In the opening scenes just after the restaurant dialogue, as soon as the scene changes there is a quick cutscene which shows the screen zooming in on the Pentagon. If you look In the lower left corner, the text on screen gives the Pentagon location as being in Washington D.C. however, The Pentagon is located in Arlington, Virginia. (00:19:02)
Continuity mistake: While the Squad is patrolling the city, the ends of Harley's bunches keep changing in style; they are straight when she's changing at the prison and on the helicopter with the Squad, really curled after Rick kills someone, then jump between straight and slightly curled for the rest of the film, with the exception of the end scene where she hasn't got her hair in bunches anymore, but a different hairstyle.
Continuity mistake: When Harley is in the elevator when the doors open you can see that her blue hair piece is coming off, but when they cut to the next shot it's secure and tight to her head.
Revealing mistake: The subway station is identified by its internal signs as "Central" station, but as the Suicide Squad enters its exterior entrance, the sign above declares that it is "Bay St." station. Bay Street Station in Toronto is frequently used for movie shoots, as it has a complete lower platform which has been out of service for decades (https://en.wikipedia.org/wiki/Bay_ (TTC) #Lower_Bay).
Continuity mistake: In the extended cut of the movie, during the final fight with the Enchantress, Harley Quinn hits her in the head with her baseball bat. A couple of shots after that are inverted, you can see it because she should be wearing the blue part of her pants and ponytail to her left side, but in these shots, the blue side is the right one.