I just upgraded my old project to new iOS 7. It was already using Cocoapods. I compile and run and everything works fine on the simulator and the device. I tried to archive
I had different problem - dublicate files.
Maybe you have dublicates in your project too. Like the ones from Pods and the other are old files which you didn't delete before you start using Cocoapods.
Double check them.
I just fixed this issue in my workspace. In my case, it wasn't related to upgrading to iOS 7; instead, it was related to archiving for App Store submission. I created an App Store configuration (a duplicate of the Release configuration), and I was trying to use the App Store configuration for the Archive action (configured under Product > Scheme > Edit Scheme... > Archive > Build Configuration). The problem was that I had created an App Store configuration for my app's project, but I hadn't created an App Store configuration for the Pods project (the project that CocoaPods adds to your app's workspace). Once I did this (again, just a duplicate of the Release configuration), the Archive action succeeded.