run pod env | egrep 'CocoaPods |Xcode|cocoapods-binary' then paste the result here
A demo project is helpful:
It will be very helpful if provides a demo project that reproduce the problem. A blank project with cocoapods-binary can be downloaded here, which can be remodeled to a minimal problematic environment. Attach the demo.zip to the comments.
Thanks for your feedback!
If it's a bug:
pod env | egrep 'CocoaPods |Xcode|cocoapods-binary'
then paste the result here