When Will does a flashback to the first time he met Emma, he is wearing a brown solid color vest. This is inconsistent with the vest he told Emma he was wearing the first time he met her (this scene took place when he was moving out of his apartment and Emma was helping him pack. Emma subsequently took the vest and wore it to school the next day, telling Will that she couldn't part with it). Will should have been wearing the gray patterned sweater vest.
Finn isn't in the first few shots of the group, but appears between Rachel and Sam without walking into the choir room.
In head-on shots during "The First Time Ever I Saw Your Face", the top strap on Rachel's dress is twisted. When shot from the side, the strap is flat as it's supposed to be.
When Sam is hitting on Mercedes at her locker, he's chewing gum--but only in the shots where the camera is behind his left shoulder.
Emma is handed four roses prior to walking into the pool area, but when Will emerges from the water to present the ring, she has at least a half-dozen.
Immediately after the "Moves Like Jagger" performance, Will almost mispronounces "Emma," starting off with a long "a" sound (as in "Amy"), then corrects himself.