When struggling with a story's structure, I think it's important to realize that it's always possible for a story structure to be executed in different ways.
Witness, starring Harrison Ford, is a good example. If you watch the film, then read the screenplay you'll discover that while both have the same story, they are quite different in execution. For example, the climax in the screenplay is quite different from the film. In the script, John Book employs a mule who kicks in the head of the bad guy, for example. In the screenplay, he lets loose a silo full of grain on him.
Now some may think that makes these two different stories, since the endings are different. But structurally, the stories are the same. What happens? John Book defeats the bad guy using his newfound Amish knowledge of the farm.
It's only how it happens that is different.
"John Book defeats the bad guy using his newfound Amish knowledge of the farm." That is a mini-story. It has a character, performing a difficult action opposed by a fearsome adversary. It's not particularly interesting in this form, but it is a story.
The how in both the screenplay and the movie are equally valid executions of the story structure for an audience. However, I suspect the film is different because it's easier to find a silo full of grain to photograph, than to train a mule to kick on cue without killing the actor.
The film doesn't violate the story, though. If John Book pulled out an AK-47 he had hidden in the trunk of his car to defeat the bad guy, THAT would have been a different story. But in both the film and the script, Book uses his Amish knowledge to defeat the bad guy. It makes them the same story, despite being very different scripts.