It looks like the way Xcode sorts file references changed in Xcode 14.*. I don't see any conflicts when my project is opened with Xcode 13.4.1 Also, xUnique claims to fix few other issues related to PBXBuildFile & SPM but it's not working for me. We may have to get rid of xUnique. Thanks @Scott for your inputs.

@Scott Thanks for your response. We have a custom script which is added as part of Post-actions under Scheme -> Build. This iterates over all the .pbxproj using xUnique and applies sorts the modified files.

@eskimo Thanks. I was looking at ~100 but i wanted to know if there is any limit or impact with linking too many frameworks.