It was due to font substitution of standard Helvetica and Times by the TexGyre ones. Uninstalling such package made the PDF readers use some pfb files in /usr/share/fonts/X11/Type1/* (Nimbus Sans, Nimbus Roman, DIngbats, ...) which seem to display ligatures correctly (at least in the supplied PDF and another one I had: both results were correct in Evince and Okular). So, I changed the target package from evince to fonts-texgyre.
In my machine, it was installed from the "recommendations" for package installation from texlive (in my case): it recommended texlive-fonts- recommended and this one recommended tex-gyre and the depending font- texgyre. Hopefully, as it is a "recommended" one this does not break anything essential outside LaTeX. ** Package changed: evince (Ubuntu) => tex-gyre (Ubuntu) -- You received this bug notification because you are a member of Desktop Packages, which is subscribed to tex-gyre in Ubuntu. https://bugs.launchpad.net/bugs/1317599 Title: Evince doesn't show "fi"-ligatures in a pdf file Status in “tex-gyre” package in Ubuntu: Confirmed Bug description: When I open the attached pdf file, evince doesn't show the "fi"-ligatures, e.g. on page 17 I only see "Preface to the rst edition". But when I mark text and copy it, the "fi" is also in there. Also printing works fine. ProblemType: Bug DistroRelease: Ubuntu 14.04 Package: evince 3.10.3-0ubuntu10 ProcVersionSignature: Ubuntu 3.13.0-24.47-generic 3.13.9 Uname: Linux 3.13.0-24-generic x86_64 NonfreeKernelModules: nvidia ApportVersion: 2.14.1-0ubuntu3 Architecture: amd64 CurrentDesktop: Unity Date: Thu May 8 18:54:09 2014 ExecutablePath: /usr/bin/evince InstallationDate: Installed on 2012-09-03 (612 days ago) InstallationMedia: Ubuntu 12.04 LTS "Precise Pangolin" - Release amd64 (20120425) SourcePackage: evince UpgradeStatus: Upgraded to trusty on 2014-04-18 (20 days ago) To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/tex-gyre/+bug/1317599/+subscriptions -- Mailing list: https://launchpad.net/~desktop-packages Post to : [email protected] Unsubscribe : https://launchpad.net/~desktop-packages More help : https://help.launchpad.net/ListHelp

