The shape is cut by a cylinder boolean object and carefully placed. Restarting from scratch works but I don’t think that is the most efficient way. If the problem involves a lot more work, it would be very tiring.
I am sure there is a method to fix it without going down that path.
enable loop tools addon (it’s already in blender just enable it in addon list) go to select the problematic loop and then press w for special menu > loop tools > circle
repeat for any problematic areas .