Touched by an 'A'-ngel - S2-E10
Revealing mistake: At the end of the episode, Emily receives a phone call from Dr. Sullivan which she does not answer. Look at her phone when she hangs up: Not only does she simply press the "hang up" icon when the arrow indicates she needs to slide it to the left, there is also a magnifying glass symbol at the bottom indicating that it is in fact an image file on the screen and not an actual phone call.
Picture This - S2-E9
Continuity mistake: When Hanna and Caleb are sitting on the swings in the park, the first part of the scene shows nothing in Caleb's lap. However, when it cuts to them holding hands, a pizza box appears. (00:29:10)
Through Many Dangers, Toils, and Snares - S2-E14
Continuity mistake: When Emily circles the word "yes" on the chalkboard, the way the circle is drawn changes between shots.
The Blond Leading the Blind - S2-E17
Continuity mistake: In the flashback to the Halloween party where Alison finds the note from A and removes it from the knife, she is either holding the knife upwards or downwards depending on the shot.
Continuity mistake: Mrs Sullivan circles "nosey bitches" on a paper (someone's file) and the circle is overlapped at the bottom. When the camera moves out the circle changes and is disconnected from the top instead.