Continuity mistake: Early in the movie when Thomas falls overboard, John Smith ties a rope around his waist (00:02:56) and jumps in after him. Thomas is very far away from the ship (00:03:12). But when the men pull John and Thomas up, John is holding on to the rope with one hand and the end is left dangling (00:03:36). One of the men who pulled them up then coils the rope with a mere two coils (00:03:48), not nearly long enough to have reached Thomas while he was overboard. In the same scene, when we are viewing the men pulling John and Thomas up from above (00:03:38) there is no extra rope at their feet as there should have been for such a long rope.
Continuity mistake: When Pocahontas sees John Smith for the first time, John is climbing up a cliff face and then a tree. You can see his musket strapped to his back as he's climbing. But after he tells Thomas he's getting a better look and then is shown in the tree, his gun has vanished.
Continuity mistake: When Meeko follows Pocahontas by jumping off the cliff, he accidentally knocks Flit, causing the bird to spin upside down. But in a wide view of the cliff in the next shot, we can see Meeko but Flit is nowhere to be seen.