When I budget check a document it gives me a "Error in Budget Check" and it asks me to click on the "Budget Options" link. It then shows me under the Exception column that "Ref'd Doc has been Finalized". What action should be taken?

Click on the "Go to Transaction Exceptions" link, it will take you to the Transaction Lines with Budget Exceptions area where you will see three tabs: Line Values, Line Chartfields, and Line Amount. 

Click the Line Amount tab and what you will need to do is delete those distribution lines the document and add them back. The document is stuck and those changes need to be updated