Preview cuts off PDF file

Hi,

When I highlight a pdf file and save it, I realize that preview app cuts the pages from margins, either from top or bottom, or from the sides. Why is this happening? Now my pdf file, an ebook, cannot be read properly because I cannot see the page numbers at the top right anymore because all pages are cropped. Can I get my pdf file back to its original undistorted form? Note that this has nothing to do with printing. I wanted to mention this because a similar problem is reported by many when trying to print a pdf file. My problem is only about highlighting a pdf file. When I highlight, the pdf gets crippled from sides.

Thanks.