I am using Moodle 3.0 and have both the Mathjax and glossary autolinking filters turned on. I have found that if a label contains LaTeX then glossary autolinks do not show up. If I remove the equation, the glossary links reappear. Glossary links in labels without any equations in are fine.
The Mathjax filter is presumably interfering with the glossary filter in some way - is this a bug?
The same problem does not occur in quiz questions, or in the Book module - just labels as far as I have seen.
I tried moving the glossary filter to above the Mathjax filter in the filters list, but this had no effect.