How to solve this issue ?

My directory structure is like this:

ModuleName.xcodeproj
ModuleName-| Cache | Cache.swift
           | Other.swift
           | project.yml

And project.yml is like this:

  sources:
        - path: ../ModuleName

the project.pbxproj is like this:

37A939F6615B5BA91AE2A93A /* ModuleName */ = {
            isa = PBXGroup;
            children = (
                36E07E7F6383BA23F4B8E79C /* Cache */,
                3789EBB3D0FCEAE7EC3CF6EE /* Other.swift */,
...
}
 
4198CE16A3FB7B27105EF115 = {
            isa = PBXGroup;
            children = (
                36E07E7F6383BA23F4B8E79C /* Cache */,
                5C3044C94C89DDAD031C461E /* ModuleName */,
 ...
}
 
...
mainGroup = 4198CE16A3FB7B27105EF115;
...

So xcodebuild is saying that "The file reference for "ModuleName/Cache" is a member of multiple groups ("ModuleName" and ""); this indicates a malformed project. Only the membership in one of the groups will be preserved (but membership in targets will be unaffected). If you want a reference to the same file in more than one group, please add another reference to the same path."

How can I resolve this ?
I tried createIntermediateGroups true but it didn't work.

Start by comparing the sources entry in project.yml with the ModuleName and mainGroup entries in project.pbxproj, including the createIntermediateGroups setting. Reproduce the generation and run xcodebuild; done means the generated project no longer reports that ModuleName/Cache belongs to multiple groups.