The length of Rick Flagg's hair constantly changes from short to medium revealing that those specific scenes were re-shoots.
When Enchantress brings the binder from the Weapons Ministry Vault in Tehran to the Chairman, he opens the book left to right. The book would be all in Persian, meaning the folder would open right to left, following Persian script.
When introducing the squad, Killer Croc's activity report states he was over seven feet tall at his latest incarceration, although throughout the movie he is near the same height as everyone else.
The admiral Waller has dinner with has a name tag on his uniform naming him "MacKensie" but the credits name him "Olsen."
When the helicopter heading into the city, the camera shows Harley holding a phone with a message from Joker. A close up of her hand shows her thumb and thumb nail bare. A few scenes later when they begin to shoot the cannon fodder, Harley's nails are painted.
June Moone's last name is spelled "Moon" in the credits.
Military-grade explosives do not explode when shot at; they require a blasting cap to be set off. This is a safety feature of such materials. Deadshot would know this with his expertise.
Jared Leto's real tattoos are visible in multiple scenes. Most notably, the triad logos on both of his forearms are seen through the shirt during the strip club scene.
When a car arrives at a building, Waller's bodyguards are egregiously deficient. As she exits her vehicle a guard armed with an automatic rifle allows her to cross in front of him, blocking his view and putting his primary in a potential crossfire. Moments later she approaches a door flanked by two similarly armed guards, both of whom turn their back on the threat zone to open the door for Waller--who is perfectly capable of opening a door for herself. These are both major breaches of bodyguard protocol.
Joker's skin and hair are the color they are as a result of being exposed to chemicals, hence why he still looks that way in Arkham. But when his hands are shown, they are flesh colored instead of white.
Just before Incubus knocks a HMMWV onto him, a US soldier is seen firing at Incubus with his M4 carbine, but there is no sound for the undoubtedly loud gunfire.
After Diablo is knocked away by Incubus (just before taking his demonic form) the scythe tattoo on his forehead has switched from facing his right to his left, meaning the image was mirrored.
At the 20th minute the overview of the Pentagon is shown with the narration on the left bottom corner "THE PENTAGON WASHINGTON DC" - the Pentagon is really in the State of Virginia.
Harley Quinn is thrown half through the windshield of the Jokermobile. The glass is broken like plate glass, while a real windshield is made of laminated glass, and does not fracture into large shards as shown.
When Deadshot first sees the Enchantress' soldiers the camera goes to a medium close up of him, with Harley Quinn's hand on his shoulder. After the camera cuts to a close up of one faceless soldier, it cuts to back to Deadshot where Harley Quinn walks up behind him and then rests her hand on his shoulder.
When Harley Quinn falls from the chopper, lands on the roof, rolls and then begins running again, it is clearly a male stunt double.
When Harley Quinn abruptly gets off Monster T's lap in the club, she walks over to Joker and has her back to Monster T. But, in the very next scene she is already sitting down behind Joker when he walks over to Monster T.
The color saturation and styling of Harley Quinn's hair changes drastically and inexplicably between scenes. Most notably, when the squad is given their equipment and clothing to change from their prison garb, her hair is suddenly smooth, curled on the ends and the colored ends seem to be much brighter. Later, after the battle in the rainstorm when dried, her hair is once again curled neatly at the ends of the pigtails. This is physically impossible without styling.
In Captain Boomerang's Activity Report being presented by Amanda Waller at the beginning of the movie, the first line of the second paragraphs calls him "Hawkness" instead of "Harkness". Elsewhere in the report, the name "Harkness" appears correctly.
Despite the fact that they were the only members wearing full restraints during the crash of the Suicide Squad's helicopter, the flight crew itself does NOT survive the crash. And this is made even more incongruous by the fact that the helicopter crashes and then rolls in a manner where its cargo area, and not flight deck, took the brunt of the impact.
When Deadshot is practicing with weapons while still being incarcerated, no one is wearing hearing protection. This is required in any facility where firearms are shot, and it surely should have been enforced in a government-run prison facility of all places.
When Deadshot has to kill a mob informant he shoots his gun which purposefully ricochets off a metal plate to kill the informant as he is walking in the hallway. As the mobster goes down there is a guard walking directly behind him. The guard would have been killed first.
When Harley is laying on the table and asks "What are you gonna do, you gonna kill me, Mr. J?", from her POV The Joker brings the shock prods outward while opening his mouth wide but in the very next cut (different angle) his mouth is almost shut saying "Oh I'm not gonna kill ya...".
The HMMWVs being used by the Military in their unsuccessful attempt to 'contain' Incubus at Midway City all seem to be the early, unarmored M1025/M1026 versions, as distinguished by the distinctive X-patterned door, the absence of a proper gun turret, and the flat 'snout' of the vehicle. By the time of the film's release, these have been relegated mainly to training facilities, Military Police, or rear-echelon units; frontline combat units, even National Guard ones, are currently equipped with the up-armored M1151 Enhanced Armament Carrier version, which looks significantly different from the M1025/M1026s depicted in the film.
In the airport dressing scene, Harley is clearly wearing fishnet tights. Less than thirty seconds later in the same scene, her legs are bare. The tights appear and disappear throughout the remainder of the film.
Harley Quinn's nail polish appears, disappears, and changes throughout the film, even within the same scene, indicating multiple re-shoots. The changing length of her nails in various scenes suggests this also.
Griggs refers to his men as guards rather than COs (corrections officers) or officers. On the sign for Bel Reve it says Special Security Barracks, a military installation. As a military installation all personnel are corrections specialists and would be referred to by their individual ranks, collectively they would be referred to as guards.
The Browning M2HB .50 caliber machine guns fitted to the HMMWVs seen in the film seem slightly smaller than their real-life counterparts, and appear to be mounted on a mount more fitting for the smaller M60 general-purpose 7.62mm machine gun.
In the airport Harley Quinn has long, bleach blonde hair. After putting on her t-shirt, it is now much shorter and has multi colored highlights.
After the main fight, when Waller shows up, she is holding her phone with the kill app horizontally. In the next shot, she holds it vertically. Then again horizontally in the next shot, although she does not move.