Multiple Alerts for Single error in interface is a design not issue with XI
This is constraint of alert mechanism in XI.
You get multiple alerts for single error,the reason is that since XI will try multiple times to process a failed message so each time it fails in its tries it will send an e-mail.to stop this the "Suppress multiple alert" box is checked but what it does is that it stops all the alerts of that specific rule until the first one is confirmed.Personally i myself (and other experts too) suggest to leave the box unchecked coz its better to get tons of mails for a specific error rather than not getting any e-mail and thereby wasting time in tracking/solving the issue resulting in revenue loss to client.
As per above comments is it possible to write an ABAP code so that we can stop multiple alerts to be sending to inbox. I am sure if we can delete message from some table then we can stop sending multiple messages to alert inbox and to the subsequent mail id also. I am not sure how alert being generated. I know where they get logged in this table sxmsalertlogger. If someone know how it works in background please let me know the table names.