Continuity mistake: In the side mission Creature Of The Night, Francine Langstrom is shown as deceased in Batman's detective mode, so there's no way she can be alive later as shown.
Continuity mistake: When you find Gordon in the mall he's wearing his jacket. When you rescue him just after your final fight with The Arkham Knight he's not. Then he's got it back later at the asylum.
Continuity mistake: In both Arkham Origins and Arkham City Mr Freeze is bald. Yet here he's shown to have strands of white hair in the DLC mission In From The Cold.
Continuity mistake: This takes place a year or so after Arkham City. Yet Joker's Titan poisoning marks look different, more like blood stains.
Continuity mistake: This is in the same universe as the other Arkham games yet Poison Ivy's gone from being green in Arkham Asylum and Arkham City to being just regular looking in this game.
Answer: All the villains financed the Arkham Knight: Penguin, Two Face, Harley, Scarecrow. This is why Two-Face and Penguin stayed in Gotham and risked getting gassed to rob banks and run guns; they'd dangerously low on funds.