The first three prototype battle flags had 12 stars. By tradition the silk for the flags was dress material donated by the ladies. The 12 stars represented the 11 Confederate states and Missouri, which had seceded, but not yet a member of the C.S.A. The 13th star was added upon Kentucky's admission.
The federal tyrants only recognized 11 Confederate states. The damnyankees did not recognize Kentucky and Missouri. The CSA recognized 13 states and 2 territories. There was a loyal Confederate government in the Arizona territory and the C.S.A. had treaties with the 5 civilized nations (Cherokee, Chickasaw, Choctaw, Creek, & Seminole) of the Indian territory, later to be Oklahoma. Seems the Indians didn't like the blue coats either, wonder why. About 3,000 Indians fought for the C.S.A. The last Confederate general to surrender was Stand Waite of the Cherokee nation, and the last Confederate civil authorities to surrender were Governor Winchester Colbert and the Council of the Chickasaw Nation.