Little Big Man is another example where the Indians are the good guys and the American Army are the bad guys.
He didn’t specify that the non-American side had to win. Getting thumped from the the POV of the enemy still counts. 
The 1962 Korean War drama War Hunt featured an American soldier who slept all day and crept out at night to slit throats of the enemy. Definitely not a rah-rah take on the US war effort. First film with Robert Redford.
I just got home from watching Fury and it didn’t make any attempt to present anyone in a good light.
We Were Soldiers shows both the American and North Vietnamese sides of a battle, rather even handedly, too.
What about Apocalypse Now? Pretty expressly showed the Americans as, basically, bad guys. Did not really show the Vietnamese POV though.
The Book Thief is not a military movie, but it is a WWII movie. And I actually haven’t seen the movie version, but I did read the book and I know the movie exists.
The protagonists are German and most of the characters are non-Jewish Germans. Some are pro-Nazi but most are not. The Americans only really come in as kind of a faceless other side. Friends and relatives are killed by the Americans and they hide from the Americans’ air raids and so forth. The only truly villainous one is Hitler, of course, but the Americans aren’t really portrayed as heroes. They’re just the guys on the other side- the ones bombing the city.
A lot of Civil War movies, especially ones before 1980, subscribe to the Magnolia Myth and portray the United States Army as evil in their battles against the Confederacy.
Not really, they’re more a faceless force that destroy the protaganists’ unit. Much like the North Vietnamese in Platoon really. It’s a good movie, well worth watching.
Das Boot - Portrayed from the point of view of a German U-boat during WWII.
Valkyrie - Actually the Allies don’t really appear at all, except for the brief battle in the beginning where von Stauffenberg is wounded.
Yes, I believe acclaimed documentarian Michael Bay encountered a similar problem filming his series on the Cybertron Wars.
With current technology, filmmakers can create whatever cinema army they want.
The main problem with those stories is making the enemy appear sympathetic as protagonists. Like you have to be a Nazi who tried to kill Hitler or a relatively low level German, Japanese, Vietnamese or whoever soldier with the worst, most dangerous job in their military.
And even then, the Americans or our Allies won’t necessarily be the “bad guys” so much as a faceless force of nature battering the protagonist from afar.
A Midnight Clear
Late in WWII a group of German “soldiers” (old men and young kids) tries to surrender to a group of Americans but it goes badly.
Terrific film. Wasn’t a big hit.
I thought of that one, but it’s a German movie, not a US production, as specified in the OP. (There were apparently plans for it to be a Hollywood production with a US director or star, but these fell through.)
Alternate title: Dances with Smurfs.
Well, what about, say, the Spanish-American War? It was a relatively modern war, it’s easy to make a case for it as an instance of American naked aggression and expansion by conquest, and nobody who knew anybody who fought in it is still alive.
And then there’s the Mexican-American War . . . no, let’s not go there . . .
The movie Unthinkable with Samuel L Jackson might fit the bill. It is not strictly a military movie, and the IMDB site quotes it as a psychological thriller, as the US has a terror suspect in custody and at what lengths people will go to get the information.
High level military officers and the FBI are involved. No fighting between opposing armies.
The Scottish protagonist was assisting the SEALS in their mission to neutralize the former military turned mercenary types being led by a rogue US Marine who had taken over Alcatraz.
You mean like the Marines who callously gun down the two Japanese POWs? But I see your point. The marines are generally just “The Enemy” throughout the film with a few exceptions, good and bad.
Didn’t “The Enemy Below” treat both sides sort of evenhandedly?
The General by Buster Keaton. Big budget, American made, and Buster was a good guy on the side of the CSA (though he was a civilian for most of the movie - the army wouldn’t take him). He got his train engine back from the Yankees.
One Man’s Hero, starring Tom Berenger, about the San Patricio regiment, a group of Irish-American Catholics who deserted from the U.S. Army to fight for Mexico.
imdb lists it as a Spain/USA/Mexico production. I suspect Spain and Mexico contributed the lion’s share, but there were American companies involved.