I had the same problem. It looks like these colors have been deprecated, but Xcode isn't upgrading them properly.
I fixed it by opening up all my storyboard files in a text editor, and find/replacing groupTableViewBackgroundColor with systemGroupedBackgroundColor, and tableCellGroupedBackgroundColor with secondarySystemGroupedBackgroundColor. Then, I opened each storyboard one more time in Xcode. This time it properly removed the duplicates, and I'm not seeing the errors anymore.
cvasselli
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For anyone who finds themself in this situation and is confused about how to remove the group identifier from the old account, the trick is to switch to App Groups from the filter on the right on the "Identifiers" page of "Certificates, Identifiers & Profiles". By default, it only shows App IDs.
This link should go their directly:
https://developer.apple.com/account/resources/identifiers/list/applicationGroup