Plot hole: McKittrick says the computer will not accept the launch codes unless they are at DEFCON 1. At the end of the climax the computer is trying to guess the code while they are at DEFCON 1. So why couldn't they just go back to a different DEFCON before the correct code was guessed?
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?
Plot hole: Given the number of possible combinations the launch code could be (over 3600 trillion possibilities) it makes no sense that W.O.P.R cannot process that significantly quicker given how easily it's able to calculate thousands of ICBM impacts, damage inflicted, casualties, etc. for each "War Scenario" at the end as quickly as it does to determine a winner.
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.