You could merge multiple PDF' into one to prepare a booklet and then with batch processing you could crop white border out of each page.
You would need to use Action Wizard to perform batch processing and then run "crop pages" command to cute the white border from every page.
Try that and see if that helps.
I think those are bleed areas, judging by the size of it.
For print, it's okay to have them. If the PDF is intended for screen use, then you can just set the bleeds to 0 pt (or picas, if you're using InDesign).