When Francis pulls over, his window is open and closed between shots.
Malcolm has dropped Dewey out of the window as evidenced by the net curtain hanging through it. However, when viewed from outside, the sash window is open wider and the curtain hangs straighter and more vertical.
Outside the bedroom window Hal shows Dewey Mrs. Johnson's cat. Dewey's left arm changes position depending on camera.
A split second before Malcolm is about to smash the microscope, you can see it being pulled away.
Reese punches his own face. First he bleeds from the mouth then not.
When Reese throws the cover off the bed to look for Dewey there is a crew member who clearly reaches out to grab it.
The grown ups closed the front door when they left and Dewey never opened it. How could it be wide open when Jellybean escaped.