Its been a few months and you may have sorted this out, but I came across this today as well.. Seems I have 2 out of 7 lessons that just don't want to export out the pdf.
So I would say there is something within the coding of HTML within one of the lesson pages throwing an error..
As a quick fix if anyone comes across this thread again (google is your friend in times like this). The quick work around is to install the EPUB exporter for Lesson modules by Steve as well, then convert this to a PDF and import it in to the lesson manual.
As a note if you don't have admin rights on your system, have a chat to your tech as they can adjust the the Moodle version to 3.1 if you are running a higher version ( so you can pull this plugin in, as its working on our 3.3 version).
As a note from Steve's github (but an easy work around once you have pulled it in to a pdf creation program)
"Please be aware that security applied to the PDF documents will not be effective if you also use the EPUB exporter for Lesson modules as EPUB has no standard security measures available at the time of development."
Hope this helps save someone a mornings work as its little things like this that can get away from you.
Thanks to Steve for releasing this set of plugins.. should be a core component of Moodle as lessons take weeks if not months to create and a document as a backup is a critical component of this process.