Audio problem: When Jennifer gives David a ride home near the beginning of the movie, you hear David's dog barking. In the next shot, we see the dog is running down the front path and it barks a couple more times. Look closely at its mouth, it's not barking.
Audio problem: When Jennifer gives David a ride home near the beginning of the film, as David gets on her bike, she looks round and tells him to "Hop on" without moving her lips. (00:18:20)
Audio problem: In the scene where the plane carrying Matthew Broderick is landing in Oregon, the plane shown landing is propeller driven. The sound effect is a jet engine aircraft.
Answer: While merely speculation, the WOPR is not alive and knows only what it's been programmed to do. It would have no concept of life or death, and as such would see no difference between the simulation and the real thing. That being said, an easy way to make it see the difference would be to program it to not waste physical resources. It would then see the use of all its actual warheads as less desirable.