This bug was fixed in wyUpdate 2.6.6. The problem was that the self-update step could get caught in a state where the new version of wyUpdate didn't extract. Your user can fix this by just shutting down your app and starting it again. The AutomaticUpdater should continue where it left off and finish the extraction of the new version of wyUpdate.
If you're using a newer version of the AutomaticUpdater (2.6.9), why didn't you include the latest version of wyUpdate?