I've had a few messages that were stored in my inbox and were older than 30 days. I've noticed that when I actually delete them they aren't moved to Deleted Items (and sat for 30 days before permanently deleted). It seems that the actual date of the email is being used to calculate the age and not the time it sits in deleted items.
iPhone 4S, iOS 6.1.3
If deleted email isn't being moved to the trash you might want to go to icloud.com from your computer, open mail, click on the gear-shaped icon on the top right and choose preferences, then confirm on the General tab that you have checked "Move deleted messages to" and selected "Tash" from the drop-down list.
Other deleted messages are going to trash -- above suggestion was already applied. Problem is specific for messages that I received more than 30 days and are in my inbox.
Strange. No idea what would be causing that. You would probably have to talk to iCloud support to get it resolved.
Messages older than 30 days in inbox are not moved to deleted items when removed.
