The Wind and the Lion does not have any really good guys, but it does culminate in a U.S. invasion of Morocco.
If we’re counting books/movies in which the US Army massacred innocent Indians, there’s Little Big Man.
(bolding mine)
[nitpick] It’s Nicaragua, actually[/nitpick]
How about the Wool series, by Hugh Howie? Post Apocalyptic-
And it turns out the US intentionally engineered the catastrophe
It’s been a while since I saw it, but it’s my memory that Three Kings is somewhat like this. At least, the more the central characters shift from their initial amorality towards being morally responsible actors, the more they find themselves on the wrong side of those in a position of authority, including their own hierarchy.
Certainly not the book — it was written by Graham Greene, a Brit.
ETA: Ninja’d! I’ll add a factoid, then. There have actually been two Hollywood adaptations of the book in all. In the original adaptation, which Graham Greene disavowed, the American is in the right and the British journalist is the villain!
I’d say the US is more like some ominous force of nature in that movie, not really a villain per-se.
That occurred to me this morning, away from the board. There have got to be plenty of examples set in the Civil War.
Maybe The General by Buster Keaton?
Maybe The Outlaw Josie Wales?
Have not been able to recall enough to Google effectively, but there was an old SF short story in which there’s some sort of US and Soviet nuclear exchange. A space platform of orbital missiles sends out the message that its missiles will NOT be fired at earth, because someone has to survive, and they would rather lose the war than destroy earth entirely. The big reveal is that the message is Soviet – they prove willing to take on for the team when the US doesn’t.
I wouldn’t say the Americans are villainous in the movie, just varying degrees of cynical or misguided. Outside of the question of the morality of the war itself, individual Americans are never shown committing any overtly immoral acts, aside from stealing the gold. And even that was gold that was taken from billionaire Kuwaiti plutocrats, so it’s not exactly like they’re taking bread out of anyone’s mouths.
Nowadays, it would seem that the task of finding American-written stories in which the Americans AREN’T the villains would be the harder job.
By the way, the story in Sailboat’s post was by Arthur C. Clarke, a Brit, hence, it doesn’t count.
Whoops, Americans, not the Alliance. Never mind.
Hey, you have to think on the overseas markets… 
What I have seen more is stories were Americans are not just the only heroes like in Pacific Rim.
But Wikipedia, which is never wrong, says he tried Mexico in 1853. It was only in 1855 he tried Nicaragua.
Remember, Walker was such a dynamo they needed ED HARRIS to portray him.
“International armed conflict.”
I’m honestly not sure whether this fits in or not, but Superman: Red Son is an alternate history where Kal-El landed 12 hours later in the Soviet Union, and grew up to be a good Soviet citizen in a Soviet Union that grows to encompass the entire world, except for the USA and Chile. The US is certainly presented as the villain in the first part of the story, but then a lot of other stuff happens, and the end is Not So Simple.
Science Fiction trilogy “Stark’s War”. wiki link
The moon has been colonised for mineral extraction mainly by other nations, the U.S. tries to muscle in and seize one of the operations. The U.S. military dudes involved eventually mutiny, and set up their own political entity.
I picked that story up because I’m interested in the Cold War and it sounded interesting. While it had its moments I don’t think it made best use of its premise and one aspect left a very sour taste in my mouth:
Namely Red Superman using implants to control the minds of those opposed to him, sorry but that’s just weapons-grade Evil and tainted the point that Superman is supposed to be fundementally decent and a good guy, though somewhat misguided, even after being brought up in an evil regime…on a counternote they depicted Red Batman as using terrorist attacks to achieve his aims but doesn’t kill Superman when he has the chance?)
I also found it surprisingly sloppy produced in places.
Oliver Wiswell, by Kenneth Roberts. A historical novel about the American Revolution, told from the Loyalist point of view.
At least from Washington’s perspective, don’t think it was that simple. The US never recognized the legitimacy of the Confederacy as a sovereign country.
Interestingly enough, in real life, several churches in Northern Virginia were vandalized by (Union) US Army troops during the Civil War. One of the churches, Christ Church in Alexandria, has refused to erase the vandalism even down to the present day and it is still there.