Apologies if this has already been reported but I couldn't find in the tracker...
Glossary items displayed using the glossary filter via the AJAX popup do not have filters applied to the text.
1. Enable Glossary and Multimedia plugin filters
2. Create glossary and add entry called 'mp3'
3. Using the MoodleMedia button in the definition text add an mp3 file and name test.mp3
4. Create a Moodle resource page and put in text content 'mp3'
5. Access page and select 'mp3' (which should show as a glossary definition)
6. A popup appears with the definition, but shows the text test.mp3 instead of the media player (and links to: @@PLUGINFILE@@/test.mp3)
Looking at the code in mod/glossary/showentry_ajax.php the results of the request seem to get returned directly from the database field for the glossary entry, filters are not applied.