I had the same issue. We have a static library that we sign&embed.
This library has some dependencies on some CocoaPods.
I was able to solve this issue by rearranging Build phases in my Apps Targets Build Phase settings.
Correct order was as follows:
Compile
Copy Bundle Resources
Copy Pods Resources
Embed Pods Frameworks
Link Binary With Libraries
Copy our Static Framework (embed & sign)
Hope it will help anyone...
Derphooks
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