For many reasons that others have outlined (historically portrayed insultingly, stereotyping, being displayed as less-than-human) along with one they haven't, which is found in the term "Native American" itself.
Saying a "Native American" skin is like saying a "European" skin. There were so many, still are so many, Native tribes and nations in North America -- some share ideologies and beliefs and cultural practices, others don't. When someone creates a "Native American" anything in media of some sort, they are actually saying "this is what I think Native Americans are like, and what they think, and how they act, and this is how I'm going to portray it."
Looking at that Sejuani alone, she is wearing a feathered war bonnet. This is common among the Plains Indians, a group of Native American and First Nations tribes, but is only worn by men who have earned a lot of respect in their tribe. Doesn't apply to all Native Americans though. See how her boar has a dreamcatcher on it? Dreamcatchers (are believed to have) originated from the Ojibwe people, and was later adopted in the 1960s and 1970s by many, though not all, Native American tribes and Nations as a symbol of solidarity between the Native peoples of the Americas. There is a significant number of native people who feel dreamcatchers are used incorrectly and have had their cultural significance forgotten, especially by non-Natives who just buy them and have them because it's what they're into that month. This Sejuani is also wearing an (extended?) breast plate with hair pipe, but the hair pipe beads were not typically used for armor - they were decorative in nature primarily. And they were not used across all Native tribes and Nations in the Americas.
I hope this has provided insight the other posts might not have.
If Riot was interested in making a skin inspired by a Native American tribe, I would hope they get into contact with a representative from their target tribe or Nation before appropriating symbols (especially sacred ones!) into a character skin.