This is a known issue with the new build system of Xcode 10.
There are radars about this and cocoapods developers are aware of the issue.
In the meantime (because it is not gonna be fixed anytime soon), you can indeed switch to the legacy build system (or clean your build folder each time you want to recompile your example app).
Another option might be to disable cocoapods input/output paths, but it is not recommended.
Please note that switching the Compilation Mode build setting from Incremental to Whole Module will in fact not work as intended.
For more information about this you can check the following issues :
https://github.com/CocoaPods/CocoaPods/issues/7966
https://github.com/CocoaPods/CocoaPods/issues/8073