This scenario can happen if you give a user a license and then press F5 say a few minutes later to refresh the page to maybe check if they have registered.
Check the Latest Activity Logs section from the Statistics tab to see if there is an entry saying the customer account was edited at the same time.
If there is then you have pressed F5 to refresh the web page resending your last command again (i.e. the granting of an additional license). Make sure you press the Details button to refresh the customer record.