Plot hole: It is revealed that Malia has been living as a coyote for eight years but earlier in the season it's shown that all shape shifters lose their powers and becomes human during a lunar eclipse, which happened in the midseason finale. So why didn't Malia turn back?
Over My Head - S3-E4
Plot hole: Daphne was able to hurt Duke because his name appears on her cell when he called, but names only show up on a cell phone if the person's number and name are programed into the phone, and Duke has already said he doesn't know her.
When the Guns Come Out - S3-E6
Plot hole: Raylan has a hunch that Winona took the money again from the evidence room, so checks the locker, finds the empty box, and assumes she stole it. When they returned the money in the previous season, he said "Put it back anywhere except for where you found it", so as to make it easier for someone to assume it had been misplaced, rather than lost. So the locker being empty is hardly a smoking gun for him to assume Winona's taken the cash.
Plot hole: After Grant finishes her video confession, Latif puts the video recorder in his cargo pant pocket. A few scenes later, he's blown up without ever having taken the video camera out of his pocket. He was at the epicenter of the explosion and he and his clothes were very much on fire, which should have completely destroyed the video camera and its recording.
Plot hole: Episode 1: All passengers on cruise ships have a passenger card with their name and cabin number imprinted. They are not just identical key cards like in hotels.
Plot hole: Early in the show, Jamie is in a patrol car escorting a witness when they are attacked by several guys in a van. The side windows of their cruiser seem shatterproof and withstand many bullets, while the rear window is shattered immediately. NYPD cruisers do not have bulletproof windows.