Reproducible with cocoapods 1.10.1.
This project is not runnable in any form, it is just a proof of concept in order to reproduce a bug.
Use bundle install to install cocoapods, then bundle exec pod install to install the pods.
This creates this file: Pods/Target Support Files/Pods-CocoapodsTransitiveDependencyBug/Pods-CocoapodsTransitiveDependencyBug-frameworks.sh . It includes transitive dependencies of the original pod, although the pod itself is not included due to :configurations => 'Debug'.