About halfway in, as David is beginning a chess game, Lisa picks up a white knight, puts it various places on the board and then on the opponent's head. There, though, it has become a white queen. When she returns it to the board, the piece is once again a white knight.
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Keir Dullea has pointed this one out himself. When David and Dr. Swinford arrive at the museum to find Lisa there, the car exhaust is visible and can be seen changing direction based on the wind and bad cuts.
When David and Simon are about to play chess, the board and pieces are set up incorrectly.
When David first meets Lisa and then Simon touches him, someone can be seen running up the stairs behind them (it might be Lisa, but it seems doubtful).