According to the progressing seasons throughout the movie, the two gray colts attacked by the cougar in the beginning of the movie do not age as they should have done. This is evident as Spirit and Rain return to the herd together, and are greeted by the same two gray colts who remain weanling's as opposed to yearlings.
When Spirit is returning to the herd after escaping the Cowboys and believes himself to be safe, he neighs to his herd. When everybody looks up, the twin foals who were Grey earlier in the movie are now chestnut.
After Spirit has fought the cougar and the rest of the herd runs down to meet him, there are trees in the background. The shot then goes to a close-up of the foal and when the camera zooms out to show the whole group, the trees have disappeared.
After Spirit has fought the cougar and the herd runs over to meet him, there are trees in the background. There is then a close up of Spirit and Esperanza (his mother) and a shot of the foal. Yet when the camera zooms out to show the whole group, the trees are gone.
When a young Spirit and the other colts are playing in the water, before being approached by the herd of bison, Spirit is shown drinking water by lapping at it with his tongue, as would a dog. Horses do not drink in this fashion, rather they submerge their mouths and suck at the water.
At one point while Spirit is watching Rain and Little Creek from inside the pen, you can see a bottom portion of his mouth pass through a log in the fence and linger there briefly, as if the log wasn't there
When Spirit first enters the fort, there is a group of soldiers riding their horses in unison. Spirit neighs at them, and one brown horse stops moving and neighs back. The next line of horses behind the brown horse are still walking, but don't move forward.