When Moodle converts PDFs to images for the PDF markup view, if the process is interrupted by a timeout or the user leaving or something else, upon returning, Moodle acts as if that is the correct number of pages.
eg. A student submits a PDF with 1000 pages to it. I (the teacher) go to grade it. Moodle works to convert each page to a PNG. The server times out (see MDL-57202) after generating 435 pages. Now return to the grading page again. The PDF markup interface shows "1 of 435 pages", and appears to be complete.
IMO, Moodle needs to somehow mark that the number of pages is complete, or compare the page count of combined.pdf and mdl_files pages and continue processing if they don't match.