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."
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 Alec kicks in Madame Dorothea's door, it does not match the door when Dorothea leaves and most of the door is missing. We see it after Alec kicks it in and there is clearly more door left than what is shown a few moments later.
When Valentine stabs the knife into the table after pouring his blood into the cup, it is at an angle. Later in the same scene, when Hodge sits down at the table, the knife is straight up, not at the angle it was at previously and it disappears completely by the time Jace and Valentine land on the table during their fight.
When Jace is at Madame Dorothea's his hair is wavy. In the next shot, as he is carrying Alec to the infirmary, his hair is very straight. Then, immediately after that, he goes down to the library, his hair is wavy again.
When Isabelle is doing Clary's hair, she has her hold a pin. Then we never see her get it back to put in Clary's hair. We see Isabelle's hands the whole time and she never got the pin but it is suddenly in Clary's hair by the end.
When Simon is hiding from Pangborn and Blackwell, we see 2 lightbulbs with pointy ends. After Pangborn stares hard to see if he sees anyone in the side room, we see a regular clear lightbulb in one of the sockets instead of the pointy one that was there when he walked in, and after he leaves.
When Blackwell is felled by Hodge's disc, it is embedded in his back and he falls forward. Hodge goes to the lever, never retrieving his disc but moments later as Isabelle and Simon are leaving, we see Blackwell still face down but no disc in his back.
When Valentine places the spear back into the pentagram, Pangborn and Blackwell come running into the room and start down the stairs. At least 10 seconds passes with Valentine noticing the card with the cup is gone, then they cut back to Pangborn and Blackwell, and they continue down the stairs in the exact position they were when the scene cut.
In scenes of Clary's childhood, you see Jocelyn's runes while washing her hands but they're kept hidden by longer sleeved shirts. When she's in the self induced coma, you see most of her arms but no runes.