First of all you must have noticed that the true dog does not really look like the animated one...

But especially, the true Balto, has never been a wolf dog. It was an ordinary husky, not rejected by people at all. Moreover, the film gives the feeling that there is one sled and that the driver is completely useless. In the reality, several dogs took the head one after another, even if Balto was the one who made it possible to find the way to Nome.

Then, the film does not show that many men and children died before the drug arrived in town, though it is suggested in one of the scenes in the film (coffins). But the film being intended for a young public, this is easily understandable.

Finally, it is wise to notice that if the film had really respected the true story, it would undoubtedly be much less interesting, and I think that the "feeling" of the history was still respected, for example you can take a look at the documentary (if you have a non-region 1 DVD :/) where we can see the true sled arriving in Nome: this scene is almost identical in the film, and it surprised me...