Surely the new Build System (Apple should give it a name) has a lot of performance improvements but will lead to missing Provisioning Profile issues after Clean Build Folder. By consecutively pressing Cmd + B a few times, the issues will be gone magically. This issue happens since Xcode 10.0 till 10.2.

This Provisioning Profile issue usually happens in a complex workspace, containing iOS app, libraries (frameworks that requires to be built from source), Watch App, custom notification service and share intent, unit tests, etc.