Have a look at the working board your issues appear on - are they all in the far right hand column?
Ok, pick one of the 88 issues that you think should be done but is showing as in-progress. Go to the issue view and check two things
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Ah, that answers most of it. You have set up your "done" status to be "in progress". That's why it's yellow.
Go to the workflow and edit it, changing the status category to "done".
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