Environment:
I have the same issue since I installed Xcode 8.1 beta and created a new Swift project. Currently I "fixed" the issue by unchecking the "Run script only when installing" the first time (causing a longer build time), for every following build I am able to build and run the app with the checkbox "Run script only when installing" checked. This works until I do a "pod install" or "pod update". I am eagerly waiting for an official update to Xcode 8.1, but perhaps it has something to do with cocoapods itself?