I am having a similar issue which happened both before and after updating to version 2.0.2.
I have found the cause of one bug which is when there is a space character following the title of a glossary item. This can be solved going to the edit page for that item and removing any unwanted space following the title.
The function trim() could be added to the plugin in the next update to force it to remove unwanted spaces before or after a glossary term. This is probably used on the glossary index, but not currently used to check the glossary title against posts/pages containing the term. Should be an easy fix. :)
This solved most of the problems for me, but there are some glossary terms containing special characters such as $, & and ', which do not get linked to on a page, but do get linked to on the glossary index.
I've noticed my theme converts this ' into the forward tick apostrophe.
Please see these terms for example: "$100 DOWN PAYMENT PURCHASE", "MECHANIC’S LIEN", "MERCHANTS & MECHANIC’S LIEN", "METES & BOUNDS"
Here is the glossary index:
Here is a page containing the same list of glossary terms for testing: