This may seem really obvious to some developers out there, but I'm a designer and this was my first time using Flash Builder. This will hopefully help out someone who's just starting out with iOS and Flash.
I had just finished the tutorial Hello World: Build a mobile app in five minutes and I had also been through the rigorous process outlined in Using Flash Builder 4.5 to package applications for Apple iOS devices.
As I completed the two tutorials I made a tiny mistake. The Application ID of my Flex Mobile Project was com.mydomain.HelloWorld as outlined in the tutorial. However, when I created the Apple App ID in the iOS Provisioning Portal, I put com.mydomain.helloworld in the Bundle Identifier (App ID suffix) field.
I used Title Case in one and lowercase in the other.

When the two fields are compared, case-sensitivity is also considered. So when I tried to package my application for deployment to my iPhone, I got the following warning.

I went back to the Apple IDs in the iOS Provisional Portal, but you cannot edit the Bundle Identifier. You have to create a brand new App ID.
So I though, "Why not change the Application ID in Flash Builder?"
I Googled how to do this, but I didn't find a solution.
So I went back to Flash Builder and after hunting round a little, I opened the XML file of the project.

I found the Application ID field and updated it to be the same as the Bundle Identifier (lowercase).

When I ran the On-device packaging sequence, my issue was fixed.

Leave me a comment below if this helped you out.