Darkness-Induced Audience Apathy: The developing characters being killed pointlessly midway through the film and the fact that once the Explosive Leash is disarmed everyone completely abandons the plot and runs for the exit can make it difficult to care about what happens in the movie.
Let's face it. All Waller had to do was pay one of the guards off to kill Riddler. She didn't need to call in Task Force X for this and have gotten many innocent personnel killed. As best put by Batman.
Also, if you want him dead because he knows how to defuse the bombs for the Suicide Squad members, it's probably not a good idea to send the Suicide Squad to kill him.
Even further, if he figured out how to disarm those bombs, wouldn't it have been better to just devise new ones? It's not like Riddler is the only criminal mastermind running around.
In Name Only: One of the biggest problems people have with the movie is that it barely has anything to do with the games other than some basic elements and some of the character designs, causing accusations that the "Arkham" brand was only added so people would actually buy it.
Let's not kid ourselves, Troy Baker's spot-on impression of Mark Hamill's Joker is what truly drove people to see this movie.
That and it's one of the few DC Animated films centered on the villains. Regardless of Batman's appearance.
Magnificent Bastard: Riddler. He steals critical information from Waller, convinces the Squad to help him in exchange for deactivating their Explosive Leashes, deduces Batman's presence among them, and ultimately walks away home free.
Signature Scene: The prison break action scenes with the other Arkham inmates near the end.
The KGBeast. He dies even before the mission of the Squad starts, only to prove that Waller is the one who holds the power over the Squad.
Black Spider. The guy is a Serial-Killer Killer forced to work with the very people he hates, and something of a Token Good Teammate. He has the least lines of all the main characters, and ends up only serving as a disguise for Batman before he gets killed off.
The Un-Twist: The scene where Batman swaps costumes with Black Spider is so in-character for the Bat that it would have been a bigger shock if that had actually been Black Spider. Not to mention, as anyone who's played Harley's Revenge knows, if anyone outside of the Bat Family grabs his belt, they get 50,000 volts.
Arkham is just as much of a Cardboard Prison as ever. Perhaps even more so: all doors can be opened at the same time from a monitor, several inmates (Scarecrow most notably) are imprisoned with their costumes and equipment, and not only is Bane allowed to keep his venom with him, there actually is a mechanism to inject it to him from this monitor. It's like they were asking for a breakout.
The fact that the warden uses his birthday backwards for his passwords. You'd think someone charged with securing Gotham's most dangerous criminals would use something not so easy to crack.
Waller for using Task Force X in the first place, when she could have easily bribed a guard to kill the Riddler.
Many fans found Matthew Grey Gubler to be too low-key and too young-sounding as the normally energetic and older Riddler.
Some people took issue with Neal McDonough as Deadshot, after it turned that that Deadshot's normal voice actor in the games, Chris Cox, was present — itself a part of a huge example of this trope within the greater Arkham series (namely, the series' inability to keep a consistent voice actor for Jim Gordon).