The Sand Creek, or Chivington's, Massacre, drew condemnation at the time from many sources. Chivington was with a Colorado militia, Lincoln had nothing to do with it.

Kit Carson-
" Jis to think of that dog Chivington and his dirty hounds, up thar at Sand Creek. His men shot down squaws, and blew the brains out of little innocent children. You call such soldiers Christians, do ye? And Indians savages?
What does yer 'spose our Heavenly Father, who made both them and us, thinks of these things? I tell you what, I don't like a hostile red skin any more than you do. And when they are hostile, I've fought 'em hard as any man. But I never yet drew a bead on a squaw or papoose, and I despise the man who would."

Quoted in Wikipedia from Hampton Sides, "Blood and Thunder: An Epic of the American West."
I am doubtful that Carson said this in the form given above.
I don't have the book by Sides and don't know how valid the quotation is.

Carson, as well as Chivington, was a freemason, like most officers in the U. S. Army (demitted as a member to the Montezuma Lodge No. 109, Santa Fe, and was instrumental in founding Bent Lodge No. 204 in Taos).

Carson himself is especially hated by at least two groups of Indians; the Navajo, many were forcibly removed from their lands and their orchards and livestock destroyed, and the Taos Indians who, after the assassination of territorial governor Bent, lost women and children who sought safety in the mission church in the pueblo, destroyed by Carson and U.S. troops.

Little control over the militias and soldiers in the west was exercised from Washington; decisions were often made on the spot by men in local militias and army units who had fought the Indians who tried to stop the move west into their lands by settlers from the east.

To attribute the actions to Lincoln shows ignorance of the conditions under which the west existed at the end of the Civil War.