Jocelyn slams the refrigerator door repeatedly when she is attacked in the kitchen, you see shelves fall off and bottles go with the shelves, when Clary sets the fire and uses the door to protect herself, the shelves and contents are back where they should be.
During the garden scene, Jace gives Clary an apple with a candle in it when they go to the stairwell and sit down, Clary places the apple beside her. When they get up and leave the apple is no longer there.
When both Valentine and Clary go through the portal they come out wet, but when Jace puts his arm through it comes out completely dry.
When Clary blows up the demon, the kitchen window is blown out. When Clary races back up the stairs, and starts hitting Simon (unintentionally) the window is in one piece.
When Jace is showing Clary the portal, there is light shining from the portal on Clary. But even after Jace closes the doors, there is still light shining on her even though there shouldn't be.
As Hodge is walking up the steps after letting Valentine in, he is clearly speaking, yet we hear nothing.
In the final scene when they drive away, the sound effect is for a Harley Davidson but they are on a Triumph.
When Alec confronts Clary in the hallway and tells her to leave, there are two instances where his jaw movement doesn't match the dialogue (both seen from behind): "Jace thinks he needs to save the world" and "We're a team, you're dead weight."
When Magnus says "I'll let you stay but only because of the cute one" Jace says "Thanks" and he responds with "What? Not you, the one with the blue eyes"(referring to Alec) yet both Alec and Jace have blue eyes.