Why were the Marines found guilty of conduct unbecoming and dishonorably discharged in A Few Good Men?

No, this doesn't surprise me at all. What is conduct unbecoming? The court saying they did not behave as a Marine should behave. They should have known what was being asked of them was not in accordance with the Uniform Code of Military Justice (or UCMJ). They should have known the order was unlawful, and therefor not obeyed it. They should have taken it higher in the chain of command. The reason they were not get found guilty on the more serious charges was because COL Jessup admitted his involvement. Marines have a lot of pride. They expect their members to behave in a certain way. Obviously that wasn't happening in this case and they were discharged because of it.

EDIT: While "Conduct Unbecoming ..." does apply to officers only, Article 93 of the UCMJ would allow for discharge of these two individuals. In this article, it states:

Any person subject to this chapter who is guilty of cruelty toward, or oppression or maltreatment of, any person subject to his orders shall be punished as a court-martial may direct.

Or they could also be charged under Article 81 which is:

Any person subject to this chapter who conspires with any other person to commit an offense under this chapter shall, if one or more of the conspirators does an act to effect the object of the conspiracy, be punished as a court-martial may direct.

If all else fails, there is a separation code which states:

USMC Other, for the Good of the Service

So while they may have had the verbiage wrong in the movie (see Andrew's "woops"), they certainly could have been discharged for their actions. I would bet they used the term, "Conduct Unbecoming ..." because it sounds better than "For the Good of the Service" ... but that's JMHO.

To be perfectly frank, you're asking an extremely difficult and arguably unanswerable question.

There's an old legal saying I remember from my Law degree. "Justice depends on what the judge has had for breakfast". Different days can bring different results and in a trial like this, the military officers are free to come to whatever conclusion they want within legal reason (similar to a jury).

It's certainly plausible that the officers could have seen a Code Red as something that must be followed at all times, thus excusing the officers of any sanctions. Alternatively, they might have seen the Code Red as something to follow at all times provided there is no danger to US life, or provided it doesn't exist within a certain culture. My point is that, like a jury, the military officers are free to come to whatever decision they want on the matter.

However, on a final note - it was a movie and thus I do think it's probable the scene went the way it did to provide that iconic ending.

In real life, a person with zero defense experience would never get the position Kaffee did. Not to mention this rather important snippet of information from a former JAG officer:

...although the two accused Marines have the main charges against them dismissed, they are still found guilty of “Conduct Unbecoming A Marine” and are discharged from the military. The only problem? No such crime exists under the Uniform Code of Military Justice (UCMJ). Article 133 of the UCMJ makes “conduct unbecoming an officer” a crime. But the two accused Marines were enlisted, rather than officers, and couldn’t have been convicted under Article 133. Whoops.

So I would argue that if the crime did exist, it really depends on the jury's interpretation of events. But the crime doesn't exist, so you really just have to come to your own conclusions on it!

Especially after the precedent of the Nuremberg trials, where Nazi defendants tried to present the "I was just following orders" defense (a defense that was not accepted as valid), most laws, codes and legal interpretations were changed to specifically state that complying with an order, if that order was clearly unlawful, is not a valid defense.

They were ordered to do an illegal thing, one that was clearly illegal, and they had a duty to refuse that order. They did not, so they were found guilty of not refusing to follow that order - that was the "unbecoming" conduct.

Wikipedia article about that defense

Just saw the movie after 20 years. I was surprised that all of the charges were not dismissed with prejudice. Court martial charges are generally dropped when commanders are found to have exercised unlawful command influence.