Hitting this same problem in Kubuntu 20.04.
My case is this. In /usr/share/applications/defaults.list I had this:
application/pdf=org.gnome.Evince.desktop;google-chrome.desktop

I guess the trailing ";google-chrome.desktop" was in some way added by 
installing Chrome.
Firefox says my default PDF application is Chrome, while all the other system 
components (Dolphin, xdg-mime, xdg-open) correctly say that my default is 
Okular.

After editing /usr/share/applications/defaults.list to remove the
trailing ";google-chrome.desktop", now Firefox correctly knows my
default application for PDFs is Okular. No need to restart Firefox, the
change was immediate.

Strange enough, I don't have Evince installed, but many other file types
are associated with Evince in that defaults.list file. I guess Evince is
ignored because it is not installed. On the contrary, Chrome is
installed and so it's honored by Firefox, but in this case it's skipping
and ignoring my actual system settings for PDF file association.

So, there must be some problem here.

-- 
You received this bug notification because you are a member of Desktop
Packages, which is subscribed to firefox in Ubuntu.
https://bugs.launchpad.net/bugs/1551171

Title:
  /usr/share/applications/mimeinfo.cache is used for default
  applications in Firefox

Status in Mozilla Firefox:
  Confirmed
Status in firefox package in Ubuntu:
  New

Bug description:
  See https://bugzilla.mozilla.org/show_bug.cgi?id=727422

  With Firefox, default applications are selected by Firefox using
  /usr/share/applications/mimeinfo.cache, however, this list is a system
  generated list in random order and therefor does not reflect the
  user's preferences of which application should be used to open a file.

  When I click on a pdf (for example), I want to have the option to open
  it in my default application, in my case in okular, and not in
  something else. However, acroread is invariably presented is presented
  as default choice because it happens to be the first entry in
  /usr/share/applications/mimeinfo.cache for application/pdf.

  This happens in spite of the fact that the desktop provides correct
  defaults.list and mimeapps.list files

  The comments in the firefox bug seem to suggest that firefox
  developers are convinced that firefox calls the correct gtk libraries
  to determine the correct application. If this is the case, then it is
  necessarily the ubuntu (or possibly kubuntu) infrastructure to be
  failing.

  ProblemType: Bug
  DistroRelease: Ubuntu 15.10
  Package: firefox 44.0.2+build1-0ubuntu0.15.10.1
  ProcVersionSignature: Ubuntu 4.2.0-30.36-generic 4.2.8-ckt3
  Uname: Linux 4.2.0-30-generic x86_64
  ApportVersion: 2.19.1-0ubuntu5
  Architecture: amd64
  BuildID: 20160209234513
  CurrentDesktop: KDE
  Date: Mon Feb 29 11:37:25 2016
  EcryptfsInUse: Yes
  InstallationDate: Installed on 2013-12-12 (808 days ago)
  InstallationMedia: Kubuntu 13.10 "Saucy Salamander" - Release amd64 
(20131016.1)
  SourcePackage: firefox
  UpgradeStatus: Upgraded to wily on 2015-10-23 (129 days ago)

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