Yesterday I ran into a mysterious issue. Some views pagers were completely missing and the typical fix to change the Pager ID (if there are multiple pagers on the same page) did not help (example: http://drupal.stackexchange.com/questions/48289/drupal-7-pager-not-disp…). The pager ID can be changed in the pager settings of the view.
So I had to search for a while and found a first hint here: https://www.drupal.org/node/2276165
And exactly, the view contained views_php fields!
Furthermore the issue links to this issue: https://www.drupal.org/node/2123315
We're not using search_api on the website that had the bug, but the discussion helped.
Finally I used the patch from #26 in https://www.drupal.org/node/2123315 which nearly solved the issue.
BUT: I was furthermore using views_litepager.module on this view and as I found out there is still an incompatibility with the given patch (as I documented here: https://www.drupal.org/node/2123315#comment-9298519)
So for the meantime I now switched to the normal mini pager that works with the patch and hope to find a better solution soon.