It’s not wrong to reflect on what you might do differently if you started your PhD again.
No thesis is perfect. No PhD journey can be completed without encountering problems or making mistakes. The PhD process is one of learning, so it’s natural to complete it and realise you might do things differently.
Some things could be because you realise a choice was made in error. Or perhaps you know that something went wrong. Maybe now, with the benefit of hindsight and greater knowledge, you know you would take another course of action or understand something with more clarity.
Considering what you would do differently is a great way to remind yourself that you’ve learned more than you knew at the start of the PhD. Don’t think about differences as a way to give yourself more problems and doubts. Reflect and see that your talent, knowledge and skills have grown.