Error "The workspace contains multiple references with the same GUID"

Everytime I execute xcodegen in my project, and then build the iOS app, I receive the same error

Build service could not create build operation: unable to load transferred PIF: The workspace contains multiple references with the same GUID 'PACKAGE:1YPFJ9C2MTIAXFLQNBJR1G6455KB9KR79::MAINGROUP'

I always have to close and re-open Xcode in this case, which really hinders programming.

I don't really understand how this can even happen. xcodegen basically only rewrites the pbxproj-stuff without using internal xcode APIs like xcodebuild, right? So why does the build operation complain, does someone have an idea?

I also analysed the pbxproj-changes that xcodegen applies. The weird thing is, even if there are no changes at all (because I've executed xcodegen beforehand) then I also get the same error as before.

So if xcodegen doesn't use Xcode API (I suppose), and there are no changes to the .pbxproj-Stuff, what could xcode even complain about?

Start by reproducing the failure when executing xcodegen and then building the iOS app in Xcode, comparing the generated .pbxproj before and after generation. Trace how XcodeGen handles project references and determine what causes duplicate GUIDs; done means the reported build error no longer occurs without restarting Xcode.