Curious if you have some sample PDFs that are problematic. I'm not doubting you, it's just that I would love to forward them on the the team at Apple that maintain Preview so they can determine what the issue is and address it.
Since CoreGraphics on MacOS has fairly rich PDF support, Preview can do some degree of PDF manipulation: reorder pages, delete pages, insert pages, rotate, crop, annotate, etc.
Since CoreGraphics on MacOS has fairly rich PDF support, Preview can do some degree of PDF manipulation: reorder pages, delete pages, insert pages, rotate, crop, annotate, etc.