If you have "Enterprise" in the glossary, but some pages contain the phrase "The Starship Enterprise" then it would be helpful to not have the glossary term highlighted in that phrase. Other examples would be words with meanings that depend on context, eg lookup American (definition: USA) but not North American (which includes Canada).
Secondly, have some definitions appear in the glossary but that don't automatically get looked up (no dotted border) / which would make the glossary very helpful for browsing.
This comes up a great deal on medical terms, where syndrome, disease, illness and disorder are all helpful to have in the glossary for those browsing it - but almost every diagnosis seems to include one of those words as part of the name. So they would be looked up on most pages.