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. Indeed, Spirit: Riding Free shows his son having to live with human settlements as a result of the train.
Misaimed Marketing: A figurine of Spirit, Rain, and their foal came with a description of the Bureau of Land Management's annual mustang roundups and the importance of "adopting" a wild mustang. Not only does this run counterproductive to the film's message, but the BLM's roundups routinely result in dead horses.
Matt Damon's narration is clearly going for quiet and understated, but a lot of the time, he just sounds bored. The film would arguably work better if you just took it out.
The entire scene with Rain lying injured beside the river. You have Spirit's dramatic whinnying, the face he makes when they hear the soldiers coming, and the fact that Rain looks pregnant.
Popular with Furries: Spirit is one of the most popular animated films with horse fans. The horses are all so gorgeously animated and people just love the whole 'Escaping Captivity' plot.
Uncanny Valley: The weirdly intelligent horses with eyebrows drop some viewers into it.
Visual Effects of Awesome: Horses are traditionally considered one of the hardest animals to animate, and the animators got them down beautifully.
The Woobie: The wrangler's horse that first urges Spirit to run. He only appears briefly, but his guilt and anguish when Spirit is captured are extremely palpable. It's clear there's a very sad story there.