Clicking on a master slide in the 'Used in This Presentation' content panel applies the selected master slide to the current selected slide(s), while clicking one in the 'Recently Used' and 'Available for Use' content panel applies it to all the slides. I dont think this is a good that the behaviour changes between content panels and think it should always apply it to current selected slide(s).
Changing status
Katarina Behrens committed a patch related to this issue. It has been pushed to "master": http://cgit.freedesktop.org/libreoffice/core/commit/?id=7f980b43a79168dec3172ea7b9abe52c6f354bc0 tdf#99107: Unify single click behaviour across panels It will be available in 5.3.0. The patch should be included in the daily builds available at http://dev-builds.libreoffice.org/daily/ in the next 24-48 hours. More information about daily builds can be found at: http://wiki.documentfoundation.org/Testing_Daily_Builds Affected users are encouraged to test the fix and report feedback.