Let’s make some assumptions about your PhD:
- you didn’t plagiarise;
- you didn’t falsify results;
- you didn’t try to misrepresent anything in your work.
All fair? Then there can’t really be any skeletons in your research closet. Maybe there are realisations you feel you “should” have had sooner. Maybe there are questions or ideas that you groan at having considered. None of these are shameful secrets though. You might not feel like telling everyone about them, but they don’t disqualify you.
Fundamental question about your PhD: were you honest? Yes?
Good. Then everything else helped you learn. Your mistakes have helped you grow to be the talented researcher you most definitely are.