I am having the same problem. I have updated my software to 10.11.1.
I have a multi page pdf, with larger than US Letter size pages (newspaper size). When I delete one of the pages and close the document, Preview automatically crops all the remaining pages.
On a pdf where pages have been deleted, and I crop one of the pages, the crop looks normal, but then when I print or close and re-open the document, the crop has moved to a different portion of the original page (including parts of the pdf that were not in the crop).
On a pdf where no pages have been deleted, and I crop one of the pages, it appears normal at first, but again, upon printing or closing and re-opening, the cropped space has moved to a different portion of the original page (the crop size/shape is the same though) and then the rest of the un-cropped pages in the pdf are also cropped (although not the same size/shape as the intended cropped area).
When Preview crops all these pages for me, it is not to a US Letter page shape, they are the same newspaper size shape as before but it looks like everything has been zoomed in (proportions restrained) to areas of the middle left side of every page (same spot). (Update: I tried the same processes on a Letter-sized pdf, all same problems occur.)
Now if I open one of these multi-page pdfs, delete some of the pages, close and re-open (weird cropping has happened) but then crop one of the pages (already weirdly cropped itself), close and re-open, the crop is as it should be.
I have tried multiple different documents, re-downloaded them and tried again, no difference in outcome.
Also note that when I try to print, the print preview window looks normal, but when it comes out of the printer it has the weird crop as shown on screen after closing and re-opening.
MacBook Pro, 15-inch, Mid 2009
Helpppppp