These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Inferred Holocaust: Spirit returns to his herd, but history says guys like the Colonel eventually won. Today, the prairies are mostly farmland, and wild horses are rounded up by the herdful to make room for this. Not to mention that there was a railroad line scheduled to run across Spirit's homeland, and they certainly wouldn't abandon a project of this scale just because of two exploded locomotives, which means that sooner or later his herd would have to deal with trains passing by all the time.
Narm: The bored-as-hell narration from Matt Damon, though some folks found it appropriately quiet and understated.
That Spirit survives the movie at all is a small miracle. Mustangs are hardy, but not that hardy.
The horse handling. When Spirit first comes to the Army fort, and they attempt to break him. the way they tied him down to brand him was inaccurate and hazardous. Even in the old West people were wise enough to not mount a completely wild horse with full tack, in a large rectangular arena.The way Spirit juggled them, most of the riders should have broken bones, if not necks and skulls. Not to mention the first thing an actual regiment would have done to a mount prospect: Geld him.