I can’t enlighten you but I can tell you how I stopped mine from running. This also happened after installing Cocoapods. In my main project’s Target, under Build Phases, I noticed two entries entitled Check Pods Manifest.lock and another called Copy Pods Resources.
Under both there was an unchecked option Run script only when installing. I checked both and at least for now my projects build and run fine without running the scripts.
This is kind of a crappy answer because I can’t really give you any more information, and it might not even work for your case, so hopefully someone comes along and enlightens us.
POSSIBLE EXTERNAL BUNDLE ISSUES
So I just had a frustrating experience debugging an issue where a pod installed library’s NSLocalized strings file weren’t working. Turns out it was because I checked the option mentioned above. Pods-resources.sh, which had the lines to install the bundle, wasn’t running in debug mode. It was only running when installing – of course! Something to watch out for.
More info in this question:
NSLocalizedStringFromTable not working in CocoaPod dependency