Because under the Constitution, and the Supreme Courts interpretation of the Constitution at the time, Indian tribes were classified as domestic dependent nations, and therefore, Indians were tribal citizenships, not American citizens. Their children were born in their "nations" and not in the U.S. so they were not granted citizenship. This somewhat ridiculous designation was upheld by several Supreme Court cases and was eventually done away with starting with the Dawes Act in 1887.
That makes perfect sense. They were born here but subject to another nation’s jurisdiction. Thus, they weren’t given citizenship. They were not the equivalent of the stateless slaves under the complete jurisdiction of the U.S.