The "Official" explaination of why Lee was denied citizenship in 1868, when he applied for reinstatement of his citizenship status, was that he had not submitted an Oath of Alligence. I wasn't aware that part of the 14th Amendment denied it rights to certain people which was repealed later.
But strangely the National Archive "found" Lee's oath among it records in 1970. I wonder how Lee accomplished submitting his Oath in 1970?
The United States government seems to have a way of losing things, or double dealing things, which they don't want to handle, instead of doing the right thing, in the first place. Such as "losing" Gen George Rodger Clark's expense reports, so they wouldn't have to repay him, for his expedition into Illinois during the revolution. Which secured the Northwest territories for the United States during the Treaty of Paris negociations. Strangely those expense reports, two bundles of them, which he had paided out of his own pocket to provide for the needs of his small army, reappeared in the National Archives also.