Continuity mistake: Near the end of the movie, the panel has JPE 1704 TKS showing, but when Joshua finds the launch code, CPE 1704 TKS is blinking on the screen.
Factual error: At the end of the movie WOPR tries to crack the launch-code using brute force. So far so good. When WOPR finds out one digit of the 10 digit code, the first digit locks and the search goes on with the remaining 9 digits. Then he finds the second one, it locks too and so on. Problem is, brute force doesn't work that way. It would be too easy (26 letters and 10 numbers = only 36 possibilities for one digit). Brute-Force works only "all or nothing", you can't sneak your way to the whole code one by one.
Plot hole: When Joshua is trying to guess the launch codes, it gets the characters one by one and "locks" them in. You can't "guess" a code like this. You have to get the whole thing correct at one time. Why would it take so long for Joshua to guess each character, if that's how things worked? If the code consists of letters and numbers then there's only 36 per character.
Plot hole: Why is David the only one aware that the computer is still playing the game? The NORAD people should have been aware the "simulation" was still running including the countdown. They believed the Soviets were really carrying out troop movements and bomber attacks over Alaska, did they never once look at the screen telling them "game time elapsed/remaining" and conclude none of it was real?
Other mistake: When Matthew Broderick is playing Galaga in the arcade, the game ends when he still has 2 lives left.
Factual error: When Joshua/WOPR calls David back, the sound David hears on the phone not only isn't what modems actually sounded like, but in reality, the answering modem makes the initial sound to start communications, not the calling modem. The calling modem remains quiet until it hears what start tone the answering side answers with so it can start negotiating baud rate, encoding method (FSK vs PSK), etc.
Other mistake: When David and his dad are sitting at the dining table, dad butters his bread to roll his corn on the cob. You can see that the butter melts on the corn and bread, but then he bites into the corn and finds that it is raw. Raw means uncooked and the cob would be cold, therefore the butter wouldn't melt.
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: 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."
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.