There is a good chance there has been a historical Comanche advisor that has not only already recommend changes to the script (if needed) but will also be on set to advise, so this concern may all be for naught. However...
Being 100% historical accurate would be a double edged blade for the Comanche. Since I'm not a historian on the subject, I'll use the word "accused" and just say in my research for this movie, they have been accused of having an incredible brutal side ad well. I would imagine if any of that would be depicted on film, true or not, it would be nothing like the positive light I presume Dan Trachtenberg will be shining on them.
War films. Important figures of our past. Hollywood seems to take creative liberties with historical films all the time because it makes for a better movie. And I don't really consider Skulls a historical film. It's a fictional story featuring an intergalactic hunting space alien. It's less "Lincoln" to me and more "Abraham Lincoln: Vampire Hunter". So as long as they don't disparage the Comanche, but rather portray them in a positive light, I don't personally feel this Predator film is worth getting bent out of shape over in regards to 100% historical accuracy. But that's just me.