The goof items below may give away important plot points.
In the alternate endings where Emily is in the asylum room, when Katherine comes into the room to tuck Emily into bed, there is no window in the door, but when she leaves and can't keep the door open, there is suddenly a window, revealing they are in a sanitarium.
In the alternate ending where Emily draws the picture, you can still see two heads on the one figure as the camera pans into the table (right after Katherine and Emily leave for school), but then when it shows the overhead view we see that the figure only has one head.
When Robert DeNiro's character David starts to realize that he may in fact be "Charlie", he has a flashback to pushing Elizabeth [Elisabeth Shue] out the window -- she scratches his left arm as she falls. DeNiro pulls up his sleeve to see that his arm is indeed scratched, but it is his right arm that is scratched.
If David killed his wife as shown in flashback, suffocating her with a pillow and then tried to fake her suicide by slitting her wrists, it would be immediately obvious to any medical examiner that she was killed by suffocation and then lacerated post mortem.