There are some historical inaccuracies, but it doesn't stop me from enjoying it. What does nearly stop me from enjoying it is that it appears to have only been released to DVD in the pan-and-scan format. I bought two different copies which were advertised as wide screen and they're both pan-and-scan. I find it frustrating and difficult to watch. In other respects, I very much like the movie and agree that it is under appreciated.
No movie is 100% accurate, of course. A few events got mixed up or blended together. (The death of the medicine man and Geronimo leaving the reservation were actually two separate events I think) One thing I didn't really get is why they killed Al Seiber (Robert Duval) off in a cantina gunfight when the real Al Seiber died in a construction accident decades later in 1907. (Robert Duval was great for that role).
Yes, I noticed it was a pan and scan DVD. I'd rather it be widescreen myself, but it doesn't bother me as much as I've spent to many years watching so many movies on VHS on regular TV screen and still enjoyed.
Movie actually departs somewhat from the post 1970s politically correct westerns. That is, basically, white men are crazy, swaggering "racists" than ruin everything they touch and Indians are peace loving hippies that are all wise and in one with nature. A trend that started in the 70s with things like Centennial and Little Big Man and continued into the 1990s with things like Dances with Wolves.
In this movie, the characters are a lot more complex, interesting and admirable in their own way. More realistic.