Other mistake: Despite being a deadly marksman (only a few minutes earlier in the movie he stopped a bullet directed at him shooting it off the air), Bloodsport snipes several times at the huge kaiju featuring a massive eye in the central part of its body, and never once hits it. (01:51:45)
Visible crew/equipment: Waller is telling "Task Force X" about the additional mission they need to pursue, saving Rick Flag. Watch the shot when Bloodsport repeats "Rick Flag?" and Waller replies "I know." The team is going through dense, uninhabited tropical jungle, but in the trees there are people in T-shirts just standing around looking at them. (00:31:50)
Continuity mistake: When Polka-Dot Man hurts Starro's leg, its minions cry out in pain as well in unison, but they do it holding their knee or thigh in one shot, their ankle/calf in the next. (01:53:00)
Continuity mistake: An personal assistant brings news about the attack on Jotunheim. Suarez turns towards her holding a sheet, but in the previous shot he already threw the document on the desk striking a pensive pose. (01:22:05)
Factual error: During the briefing, Waller shows the map of the island of Corto Maltese. The map positions the fictional island in the Caribbean (it says "Mar Caribe"), but she says it is "off the coast of South America." The map does have also a set of precise coordinates in one of the middle quadrants; 45°43'36.0"S 56°32'58.2"W, which would place it far west of Argentina, surely nowhere near "Mar Caribe." (00:22:10)
Deliberate mistake: When King Shark grabs the guard from behind and eats him, he screams loudly, but nobody reacts to it, not even his buddy who just went left to fetch a drink. Later Cena and Elba kill 'silently' every other guard, but when they get to a group of three that Bloodsport yo-yos to death, it's pretty impossible that those three could have missed the carnage just a little off to the left. Then again, at the end a whole tower gets demolished without anyone noticing, so It'has to be deliberate. (00:33:05)
Revealing mistake: When Bloodsport rescues Ratcatcher 2 from on top of the car, they don't actually dodge the arm coming for them but are going straight through like it's not even there. (01:54:16)
Continuity mistake: The government forces are rounding up the foreigners outside the bar. Bloodsport finishes his beer and puts it down; the bottle is facing opposite directions in the two shots, just look at the label. (01:02:10)
Continuity mistake: Seeing all the Starro drones being held captive in the "Dirty Little Secrets" section, Rick Flag says "Good God". Thinker replies "If God existed..." etc. During this sentence Flag lowers the gun slightly before the first cut, but the gun is angled higher as it cuts to Peter Capaldi and even higher in the wider shot. (01:23:05)
Continuity mistake: When the team gets to the rebel leader's tent unnoticed after a patently absurd massacre, Alice Braga is holding her cup with both hands around it. Reverse shot, and she has one hand on the top and one on the bottom. (00:36:00)
Visible crew/equipment: In the club scene when Polka Dot Man is dancing, when the camera spins around you can briefly see the top of a camera/gimbal.
Continuity mistake: Dubois is scrubbing the floor as Amanda Waller exposits to her team of analysts who is he. The rag on top of the alcohol bottle reaches the level of liquid in some shots, not in Waller's semi-POV. (00:16:00)
Continuity mistake: When Harley and not-Milton join the others at the end of the movie, shadow areas appear and disappear between shots (rather obvious when King Shark asks his first "Num-num?"). (02:01:10)
Continuity mistake: When Polka-Dot Man shoots his projectiles at his giant mom, he's standing in the sun or in the shade depending on the camera angle. (01:52:45)
Continuity mistake: When the people in the control room wake up and find out there's "A freakin' Kaiju", the clocks are showing entirely different timezones from the previous instances, with a wild difference from one another (earlier they were a couple hours apart, now we have even 9 hours), and none of which matching the time when the action supposedly takes place (it was late morning, past 10 AM as shown by the surveillance room clock and the phone in the hands of Harley's torturer). (01:46:45)
Continuity mistake: When Flag collapses after his fight with Peacemaker, his hand is off the shower tray. Peacemaker then talks to Ratcatcher 2, and Flag's hand is well on the tray. (01:31:40 - 01:32:05)
Continuity mistake: When Peacemaker sticks the detonator inside the explosive after the humorous argument with King Shark, the detonator is suddenly lower in the last shot. (01:21:45)
Continuity mistake: After killing the guards all around her, Harley rushes into the next room, kicking the door open, and begins fighting in close quarters with more. She breaks the arm of one of the guards who tries to stab her through the bars. In the sequence, the red wrap is covering her fingers in one shot, it's underneath them in the next. (01:12:15)
Continuity mistake: At the beginning of her escape, Harley faces three guards. The rightmost one is smoking a cigarette, then has no cigarette in his mouth, then he has it again. (01:11:25)
Continuity mistake: Ratcatcher 2 tries on some round glasses holding the box with her thumb on the top of the side, into the opening. Wider shots have her hand placed towards the bottom. (00:53:35)
Answer: It's a combination of various reasons. Will Smith wasn't available to reprise his Deadshot role, so there was a shift in the story. King Shark was intended to be in the first film, but the CGI was too extensive, so they went with Killer Croc. In this film, they took the opportunity to bring in King Shark as the "monster" character. But, this film isn't really a sequel or reboot. Basically, this is a new storyline with new characters, and many of the previous characters are just not in the film, with no exposition on what happened to them, and they may not even be part of this film's "universe." The fact that some of the actors play the same character in both films only serves to muddle the concept of this film not really being a part of the previous film's continuity.
Bishop73