This is a known Xcode issue with the Swift Package Manager.
Looks like it wrongly adds the SPM framework (presumably Shake) to both the Plugins directory (and other extension directories) and Frameworks directory, which
causes ITMS-90806 issue.
We believe it started happening on Xcode 12.1 or 12.2 version.
The first solution is to update the Xcode installation to the latest App Store version and see if the latest version eliminated this bug.
We've tested this on the Xcode 12.2 beta 3 and this issue was resolved.
If updating Xcode is not an option, you can try manually deleting the duplicate Shake.framework file from the built App.app archive (found in Xcode->Organizer after Archive command) and then triggering the AppStore upload.
Swift tracked issue -> https://forums.swift.org/t/swift-package-binary-framework-issue/41922
A custom Run Script Phase can be added to the BuildPhases section which deletes the duplicate framework, however this being an Xcode issue means that it will get resolved in the future releases so updating Xcode is the best bet.