Kind of a mix of things. Mysterious Native American combined with non-specific Native American, made up rituals. They didn’t really try to make Chakotay a fully realized character until later on and didn’t do it well when they tried. Add to that some of the complaints I have for a lot of the actors on the show. Robert (Beltran) didn’t get a chance to branch out and show the depth of his acting skills. Roxanne and Garrett didn’t really get to either. Tim Russ did quite a bit (and it always made for some really great Star Trek).
Some of the mistakes are ones ones X-Files made too. From what I’ve heard, the X-Files creators worked with NDN consultants to improve their representation on the show after criticism of Shapes. Unfortunately I’m having trouble finding references so I may have misunderstood what happened there.
ETA: There’s more than one Robert on the show. Clarified. 
