When Evan writes the note under the doctor's desk, he has just moved the box containing the home movies to the floor in front of him. After writing the note, he reaches forward and turns the projector on, but never sets it up.
When Evan asks his mother if she brought the journals to him in jail, she holds up two, saying that she "only found these two." When the "sisters" knock the journals out of his hands, three journals fall to the floor.
When Evan kills Tommy, the first few close-ups of Evan show almost no blood splatter (if any) on Evan's shirt and cheek, but in the last shot, when he is being dragged up by security, the blood splatter is very noticeable and prominent.
When Evan is talking to Kaleigh about her ever wondering what could've happened if they had gotten together (in the version in which Evan has no arms), Kaleigh offers him a granola bar. He tries to grab it with his prosthetic hand, but he breaks it, making the bar fall to the floor. A few seconds later he is holding the granola bar in his hand.
Evan wakes up in the institution and gets down on the floor looking for his notebooks. The shot of him on the floor shows his bed sheet and blanket hanging off the side of the bed making contact with the floor. In the following shot the sheet and blanket are no longer hanging off the side.
In the final scene of the theatrical cut (not the director's cut), you can see a grown up 28-year-old Evan as a businessman walking out of a building, talking on his cell phone. When he walks by a building, the reflection of a camera is seen moving on a tinted window.
Evan reads his journal and goes back to where he and Kayleigh are making the Robin Hood movie in her father's basement so he can fix it. While he is making his speech to her father about his decisions, during the entire monologue we can see a crew member standing in the back left mirror. If you watch closely, you can see the crew members move.
When Evan comforts his mother outside of the Psychic's building, she confesses that she had 2 stillbirths before Evan was born, and she refers to Evan as her miracle baby. When Evan is strangling himself in his mother's womb, we hear her say that she had 3 stillbirths before he was born, and she again refers to him as her miracle baby. This is not a flashback, but rather a deliberate change explained by Eric Bress and J. Mackye Grueber. It is implied that the two previous miscarriages before Evan went through the same journey, and that Andrea is saying this to her new (future) child - a girl, who has broken the family "curse".
When Evan goes to burn his journals with his buddy in the large metal can, he pours the gasoline into the can and then sets down the gasoline right smack next to the can and proceeds to light the match and watch it go up in flames. Although in Hollywood this clearly is a very dangerous move that could incite an explosion, in real life liquid gasoline doesn't explode. Gasoline must be evaporated to 1-15 ratio to air in order to explode, which is very hard to achieve outside controlled lab environment, despite what numerous Hollywood films show.
In the theatrical ending, Evan still has multiple journals though he has never met Kayleigh. Dr. Redfield suggested that Evan start keeping journals after his mysterious drawing in class and not after his incident with Kayleigh and Tommy's father. After the incident, Dr. Redfield suggested that he meet his father - not keep his journals. It's not unreasonable that he committed to keeping journals years after Dr. Redfield asked him to (hence his interest in psychology). Though the books would have been completely different, Evan's burning of them was symbolic and not literal.
The note reading "I'LL COME BACK FOR YOU" changes. Note the break between the top stroke of the I in I'LL and the apostrophe and no break in the bottom of the B of BACK the first time we see the note. When we see the note in Kayleigh's grave there is no break on the top stroke of the I and there is a break in the bottom of the B. There is also no red margin at the top of the first note. This of course assumes the note put onto the grave is not symbolic, in that, he had kept the original rather than the deeper symbolism of how, for Evan, the entire story is about going back for Kayleigh.
Evan asks his cell mate to look for his hands to proof that he can "time travel" he then travels back to when he was kid and stabbed his palms. As a "proof" he now has marks in his hands. But if he got those marks when he was a kid he would have had marks in his hands already when he went to jail (in that reality). So the marks being there wouldn't have proved anything (to anyone but to Evan himself).
When Evan is in his dorm and the room is backwards, we see Evan's profile, but for a second, Evan turns around showing that the left side of his nose is about twice as big as it should be because of the prosthetic tube used to achieve the affect of a dripping nosebleed.
When Evan and his mother visit the fortuneteller in the Director's Cut, she says that Evan has no "lifeline" and should therefore not exist. In the scene that follows where Evan and his mother sit outside the fortune-teller's Evan's "lifeline" is clearly visible in his palm.
When Evan is in the wheelchair and talks to Kayleigh, his face is desaturated (see commentary track Director's Cut DVD). The effect is visible when people pass behind Evan. Their skin-tone changes when they walk through that desaturated part of the image.
The goof item below may give away important plot points.
When Evan (at the age of 20) is sitting in his chair reading a journal after Kayleigh has just killed herself, he writes in his journal about his first time travel ("if I can make scars, do I have the power to heal them?"). Then he doesn't change the page, but when the journal is closed up, his note isn't there.