When Tyler is smashing Ryan's car he damages the driver's window and the front right headlight. However, later, when Elissa is driving the car up to Ryan's house there is no sign of any damage.
Elissa is walking home when she gets a ride from a neighbor because of the rain. Elissa's mother asks her how she got home as soon Elissa walks in. Elissa had just received a phone call while walking in which her mom that she was the working late shift. Either the neighbor took a very scenic route home in the rain or Elissa's mom should have been at work.
When Elissa is in the secret room under Ryan's house she screams, and Ryan replies that nobody can hear her, implying the room is likely soundproof. However when Peggy was in the secret room beforehand she was gagged.
When asked to join a party after school by Tyler, Elissa is called by her mum. First, she holds the phone in her right hand but after a brief cut to Tyler she holds the phone in her left hand.
In the garage scene, where Elissa finds a box in the glove box in the car, there is a cloth and a bottle of Chloroform in the box, which Ryan used to kidnap a girl months ago! You definitely can not put out a mouse with the remaining Chloroform in that cloth after that time! And even if he refreshed the Chloroform on the cloth 5 minutes ago, it takes more than 20 seconds to put out Elissa with it, not 3 seconds.
Elissa's "phone" was actually an iPod touch (4th Gen)
When Ryan goes downstairs to feed his sister, he used the key to unlock the door from the outside as well from inside, however when Carrie Ann uses the key to unlock the door from the inside, the camera pans to the outside of the door which now has a manual door lock.
When Carrie Anne is shown falling off the swing in a flashback, the actress's movements make it clear she is wearing a harness for the stunt.
When Ryan goes downstairs to feed his sister, he used the key to unlock the door from the outside as well from inside, however when Elissa uses the key to unlock the door from the inside, the camera pans to the outside of the door which now has a manual door lock.
When Elissa's mother calls the house it diverts to her cell and appears as 'Mom' on the caller ID. When the officer calls the house and it diverts it should therefore appear as a cell phone number, but in fact it says 'Home'.