I’ve that problem as well, Ari. I think I know what Peter means.
When viewing the spreads, one page will appear higher than the other. Not by a lot. I think I measured it once and it was about three or four points.
Imaging placing two playing cards side by side (those will be your page spread). Not take either card and move it up slightly. See how the cards no longer align? That is what it looks like on screen. I believe that is what Peter is talking about. And I’ve seen that happen.
Peter–was the file downsaved? I have seen that happen when downsaving several versions (i.e., CC2015 down to CS6).
If not, I have seen InDesign sometimes do weird things when applying master page–everything from telling me (incorrectly) it’s the wrong page size or it causes the spread to not align (page edges).
If it’s just regular text, I usually just delete the affected spread, go the previous page and add two pages, and then re-link and then it’s fine.
I’m guessing it’s only affecting a certain amount of pages. In my experience it’s not document wide.
I had the same thing happen to a co-worker a few days ago. I’ll ask her tomorrow which job it was (it was the one that was downsaved several versions) and I’ll take a screen shot and share here.
Note: Thankfully it was not a the actual book but a test/sample for the proofroom to look at. The book iself remained in CC2015 and was fine.
I have no idea how this would affect PDFs (or if it would). To be honest–I’ve never tested it. I’ll have to try that as well.