Adobe InDesign/Page Numbering Alignment
In Adobe InDesign, the pages numbers I lined up manually on my spreads look aligned properly---I checked to be sure before printing. However, when the spreads print, the page numbers on the right look higher than the left, as do crop marks, although document setup looks fine, and shows no discrepency between sizes of left/right pages. Very puzzled about this...
To insure accurate placement, I usually put page numbers on the Master Page. There you only have to make sure the left & right side line up once and you're all set. Once I have one page number set I'll copy and paste it to the other master page, switch the text from left alignment to right alignment, and position the text block using the margin guides.
The crop marks are put in place by the program and shouldn't move in relation to the page. This could be a problem with your printer not putting every page in the same position on the sheet.
Hope this helps,