The "alert" status typically reflects what appears for the controller status, so it will match what appears in System Manager (i.e. failed hard disk, slow fan, etc); sometimes it will appear when you don't have optimal permissions or licenses available for that controller, or that controller doesn't match what is seen for the partner.
You can view the "status reason" by clicking on the tiny arrow beside one of the headings, and choosing the checkbox beside "status reason".