I just spent several hours figuring this out.
Links to all glossary entries appeared at the bottom of all pages, regardless of template. I determined that something was injecting a div#glossaryList into the_content()'s output. Was on the verge of trying to figure out a way to custom parse the content when I noticed the "optional" glossary page id setup note in Installation.
4. Create a main glossary page (example "Glossary") with no body content if you wish to. If you do not create this page then your terms will still be highlighted but there will not be a central listing of all your terms.
5. In the plugin's dashboard preferences, enter the main glossary page's id (optional as above)
This may be "optional" for some, but if you don't set up a glossary page and assign the page id in the settings, you'll get a glossary list on every page.
Not desired behavior for most. Workaround identified. Recommend either fixing code or updating the documentation to note the consequences of not performing this "optional" step.
Love this plugin except for the time this issue cost me. (Won't stop me from using it now that I know, though.)