It looks like the bug where iPhone users had discovered emails that were deleted long time back while using the Spotlight for iPhone feature is fixed in iPhone OS 3.1.
iPhone user, Ted Landau had reported the bug in iPhone's Mail app after upgrading to iPhone OS 3.0.
iPhone user by the name of Matt Janssen had even published a YouTube video of the bug.
Justin over at WhenWillApple had reported that the issue should be fixed in iPhone OS 3.1 as he had tried to replicate the bug on an iPhone running the beta version of iPhone OS 3.1 with both POP3 and IMAP accounts and was not able to reproduce the bug. He had also published a video to show that the deleted emails are no longer displayed in Spotlight in iPhone OS 3.1:
I just tested it on an iPhone running iPhone OS 3.1 and I couldn’t replicate the bug. The deleted emails no longer show up in the search result in Spotlight (please note that the emails need to be deleted from the thrash folder so that they are not indexed and show up in the search results). In fact, even if you click on the cached Spotlight search result, it is no longer an active link to the deleted email (it doesn’t open the deleted email).
So looks like Apple has fixed the bug for good in iPhone OS 3.1. If you had observed this bug in iPhone OS 3.0, please let us know if you are still able to reproduce the bug after upgrading to iPhone OS 3.1.