Putting your own GPL code in your iOS app is fine. The issue with GPL on the iOS store arises when you put someone else's GPL code in your iOS app.
The problem is that that the terms of use that the user must agree to in order to use the store place restrictions on what the user can do with the software they obtain through the store. These restriction are at odds with the GPL requirement that you not place additional restrictions on GPL software you distribute.
For Apple to distribute GPLed software on the Apple store, the copyright holder has to give them permission to do so on terms other than GPL. In the case where the developer who places the GPL app on the store is the copyright holder to the entire app this is no problem. They have had to agree to Apple's terms for developers in order to be allowed to upload. I've forgotten what exactly is in those terms, but I'm almost certain there is something in there that requires the developer to give Apple permission to distribute.
That permission that a developer of a GPLed app (or an app under any other license) gives to Apple to make and distribute copies only applies to code owned by that developer. If they have included any third party GPL code from owners who have not granted Apple that permission, then the app as a whole will not be legal for Apple to distribute.
In summary, distributing on the Apple app store requires that you give Apple a license to make and distribute copies under Apple's terms, which are not GPL compatible. Apple does not care what license you give to anyone else, so it is fine to go with "GPL for everyone plus this special license for Apple".
