Whenever you think that a particular word should have been flagged as an error but wasn't (or vice-versa), or that an abbreviation should have been expanded or something you typed unexpectedly behaved like a shorthand, Find in References can be a big help.
Often the results from Find in References will be enough to figure out what's going on. Sometimes it won't.
Additional "debugging" aids can be found in the actual Learned Words, Shorthand Glossary (and other) document windows.
The "Show Duplicates" checkbox in the toolbar of all document windows toggles an additional column that indicates which words (abbreviations) also exist in other places.
Hover the mouse over the Show Duplicates checkbox for more detailed info.
Caution icon: The same word (or form of that word) is found in another reference, and there may be a conflict to resolve (often there isn't, or it's not a real issue). Control or right-click that word to see a menu with the other reference(s). Select a reference from that window to open it (if applicable) to the conflicting word.
Green "dot" icon: The same word (or form of that word) is found in another reference, but it's unlikely that it's causing any trouble (the reference isn't used, for instance). Control or right-click that word to see a menu with the other reference(s).
Shorthand Glossary document windows have a Preview drawer you can open as well (again, icon in the toolbar). This is by far the best way to find out how varying the case of an abbreviation (both how it's defined and how you type it) affects the actual expansion.
If you're still baffled, take a look at your Interactive, Automatic preferences (these are all off by default for very good reasons - probably not a good idea to check them all just because they exist). Pay particular attention to the "Capitalize proper names and acronyms" preference. If you were wondering why "sos" was expanding to "SOS" when you typed it, chances are good you have this preference turned on...
Find in References can be your best friend
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