Visible crew/equipment: Immediately after the scene where they are removing chairs from the launch facility and installing electronic relays, there is a panning close-up shot of the WOPR. When the camera reaches the end of the WOPR, there appears to be red fabric to the left of the WOPR that moves slightly before the scene ends. It looks like the back of someone's shirt who is sitting on the floor next to the WOPR. Perhaps this is the crew member operating the Apple II that controls the lights on the WOPR? (00:23:13)
Revealing mistake: When Joshua/WOPR is trying to figure out the launch code at the end of the movie it picks the "1" out of the 1704 twice.
Other mistake: When David and Jennifer are sat at the IMSAI terminal making the flight reservation for Paris, the date on the booking system shows as 18th March 1982, but the date of the flight is 18th August 1983. (00:29:11)
Continuity mistake: When everyone is trying to get Joshua/WOPR to stand down from launching its own missiles, McKittrick's assistant Paul is standing with the rest of the group, but then there is a quick shot of Paul looking at the WOPR and then within seconds Paul is overheard saying "must be caught in a loop" as if he's standing beside everyone again.
Other mistake: When David first logs into the system after finding the right password, it shows a phone # beginning with the prefix 936. The only problem was that earlier when his computer was dialing numbers, he had not gotten to 936 yet. That was the 4th prefix and he only got through the first 3. There is no way he could have dialed that number with his computer program.
Other mistake: Why didn't Falken just call NORAD instead of going 1400 miles? NORAD in Colorado Springs, Colorado, U.S. to Goose Island, Oregon is far (1,388.5 mi). Robinson R22 has a maximum speed of approximately 115 miles per hour. The R22 typically has a maximum range of around 200 to 240 nautical miles with standard fuel tanks. It would have to refuel 8 times, making that long 16+ hour trip before the wargame ended, is impossible (not to mention arriving 'just in time').
Other mistake: When David was having his computer dial all the numbers in Sunnyvale, he pulled up the list of numbers already dialled, and there are numbers with the prefix '936', but before he pulled up the list, when the computer was dialling the numbers, the 936 prefix was on the far right hand side. No numbers with the 936 prefix were dialled yet, so they could not have been on the list.
Factual error: As the computer repeatedly tries different bombing strategies, all resulting in "WINNER : NONE", one of the strategies it lists misspells "Israel" as "Isreal" and "Palestinian" as "Palistinian."
Continuity mistake: The 1 minute 30 second countdown takes almost 2 minutes and 30 seconds, despite it being a continuous shot. And the last 10 seconds takes at least 13 seconds, despite each number being counted down out loud.
Continuity mistake: When Matthew Broderick is first at his computer the screen is large and has an external modem on top. Later there is a close up shot of the keyboard and the monitor. At this point the monitor is completely different and much smaller. Then shortly afterwards you can see the larger monitor again with the modem on top (behind Ally Sheedy) while it war dials numbers. Shortly after that, the monitor changes again. You can also see the changes with the color and the "side handles" used for carrying. I counted three different monitors being used.
Factual error: In the first scene with the computer (when Ally Sheedy visits) Matthew Broderick puts the handset on to the modem coupler with the cord toward him, then pushes the button on the modem which is facing him. A shortly while later he is at the computer and he puts the handset backwards with the cord away from him and pushes the button which is still facing towards him. The modem would not have worked properly, since it needs to send and receive through the respective ear and mouth pieces.
Continuity mistake: When NORAD is waiting for the bombs to initially hit the bases, the animation of the inbound nukes is replayed multiple times showing the same approach towards Loring AFB.
Revealing mistake: When David begins to play against the WOPR computer, the images on the war room screens show various tactical movements by other countries. These are the same images shown the first time the war room is seen.
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.