This issue could be caused due to the following reason:
– The object that was put into Maintenance Mode is not generating the actual alert. To verify this, right-click “Active Alerts” view on the Operations Manager console and select “Personalize view” from the menu. Select the check box next to “Class” under the “Columns to display” option.
You will see a new column “Class” under the Active Alerts view. Make sure the instance of this class for that agent is in Maintenance Mode.