The error was discovered in version 2019 when working with a large file (more than 6 MB).
Between clicking the "Check for Issues" and "Reduce File Size" buttons, Visio first shows the "Loading document data" message, then "Searching for issues". There is a time interval when the "Loading document data" message has already gone out, but "Searching for issues" continues to work. During this time, Visio does not block clicking the "Reduce File Size" button. If the user clicks this button before the "Searching for issues" operation is completed, the number of unused master shapes will be determined incorrectly. As a result, USED MASTER SHAPES and THEIR COPIES on the document pages may be deleted.

Good catch.