I have a project setup with the following Targets:
1- PopFramework: iOS 8.1 framework containing ReactiveCocoa.framework as instructed in the Carthage readme section
* it has ReactiveCocoa.framework in the "Link Frameworks and Libraries" under "Build Settings"
* it has ReactiveCocoa.framework in the "Link Binaries With Libraries" under "Build Phases"
* got the "carthage copy-framework" run script build phase with the input files
"$(SRCROOT)/Carthage/Build/iOS/ReactiveCocoa.framework"
2- Pop.app: iOS 8.1 Target
* it has ReactiveCocoa.framework in the "Link Frameworks and Libraries"
* got the "carthage copy-framework" run script build phase
the Pop target builds and runs on Simulator and Device no problem.
Also it archives successfully.
The problem appears when submitting to the AppStore:
i get two errors:
Archive submission failed due to the issues listed below.
(1) ERROR ITMS-90205: "Invalid Bundle. The bundle at 'Pop.app/Frameworks/PopFramework.framework' contains disallowd nested bundles."
(2) ERROR ITMS-90206: "Invalid Bundle. The bundle at 'Pop.app/Frameworks/PopFramework.framework' contains disallowd file 'Frameworks'"
Pop.app
Frameworks\
libswiftCore.dylib
...
PopFramework.framework
Frameworks\
ReactiveCocoa.framework (Included once in the PopFramework.framework)
ReactiveCocoa.framework (Included a SECOND time in the Frameworks folder)

The PopFramework.framework should not include the copy-framework, you'll want to link them but copy them at the app level.
Hi @robb I now have the "carthage copy-frameworks" only on the Pop.app level.
That seems to have done the trick :)
Thank you so much, I've been working on this all morning :+1:
I'm experiencing the same issue. This is my Cartfile:
github "Alamofire/Alamofire" >= 1.2.3
github "tristanhimmelman/AlamofireObjectMapper" >= 0.4
@robb What exact actions do you mean by your recommendation?
The PopFramework.framework should not include the copy-framework, you'll want to link them but copy them at the app level.
@AlexKorovyansky I don't think my suggestion applies to your problem. But generally, if you have transitive dependencies, you still want to link all of them at the app level and have your copy-frameworks step there.
@mdiep I've been out of the loop for way too long, is copy-frameworks needed still with Xcode 7?
I'm using XCode6. What do you mean by this phrase?
should not include the
copy-framework
AFAIK copy-framework is still needed. It's a limitation of the App Store that binaries aren't allowed to contain the simulator architecture.
FYI, for me this workaround suggested here https://github.com/Carthage/Carthage/issues/353, looks working right
Most helpful comment
Hi @robb I now have the "carthage copy-frameworks" only on the Pop.app level.
That seems to have done the trick :)
Thank you so much, I've been working on this all morning :+1: