Continuity mistake: When Scott loses his asthma inhaler, we see it fly out of his hand and land on the ground and it is a light khaki colour. Later on, when Scott and Stiles go back to the woods in the day to look for the inhaler, they come across Derek and when Derek throws Scott his inhaler, it is a white colour.
Continuity mistake: In the scene where Scott is eating lunch and Allison comes and sits directly behind him, she sits down with a bottle of water and a bagged lunch. He has a tray lunch. Later on it the scene it changes: Allison has the tray lunch and he has the bagged lunch.
Continuity mistake: While Stiles and Scott are at the vet getting the black dust, the vet puts the mountain ash on the table and says it's for Stiles. Stiles picks up the bottle and it's in his hand. A shot later the bottle of ash is back on the table, but Stiles never put it down. Then the shot after they show it on the table, it's back in Stiles' hand and he sets it back down.
Continuity mistake: When Scott and Isaac are at the vet after helping Issac's dog, Isaac walks toward the door talking about the lacrosse game. If you look at Isaac's head, sometimes there is a tiny piece of hair sticking up and sometimes there isn't. It switches back and forth between shots.
Plot hole: We find out the coyote that has been wandering around the Tate house is actually his long lost daughter, Malia, that turned lost control during a full moon eight years prior and has been living as a coyote ever since. When Scott forces her to turn back into human for she is incapable of shifting back into coyote form. However in the season 3 mid-series finale we find out that all shapeshifters loose all their powers and becomes human during a lunar eclipse. Shouldn't Malia have turned back into human form that night?