I think I'm starting to understand what happened, but we still don't have quite enough information to help...
Is sounds like you were trying to connect your ancestor, Thomas Jefferson Baggett [Baggett-533] to his father, but you typed the wrong ID by mistake, and so connected him to the wrong parent. Correct?
Just go to the Edit tab, and on the right side of the page, click "replace/remove father". There will be a place to put in the correct ID number.