Fragmentation check is very expensive on Monitored entity hence SQL Monitor checks for this only once a week at 1:00 am on Sunday (Base monitor local time). So even if you have re-build index and the alert condition no longer exists, the alert is still 'Active' because the next check will only happen on Sunday. After the collection happens on Sunday, the alert will be updated.
Hope this explains. Let us know if you are any more question.
Project Manager, SQL Monitor.