Hi,
there seems to be a bug in the titlesec package within the ubuntu container which leads to missing section numbering in some documents. See https://bugs.launchpad.net/ubuntu/+source/texlive-extra/+bug/1574052 .
From my tests this seems to be fixed in the texlive package for ubuntu 18.04.

Another possible fix is described here: https://tex.stackexchange.com/questions/299969/titlesec-loss-of-section-numbering-with-the-new-update-2016-03-15 .