Exactly the same issue.
I have 120 commits changing code over to SWIFT3 ... one of them has cause issues, and I can't work out if it just one of the Unfixed SWIFT3 bugs, or it is something in my own code.
What is the point of being able to commiting-mutple-files at once in Xcode's code management system .. if you are not able to Uncommit the multiple-file-change?
If Xcode is going to fix this (rather basic functional Bug), may I suggest that they put up a large Banner when you are commiting, to say "Note: Committing files here doesn't actually do anything to help you recover back to this safe point, you'll need to learn low level commands and spend days hoping that everything works again in this project."
Is Apple is trying to push people to make Hourly snapshots of their entire code repositories .. just incase you need to revert back to see the POINT IN TIME that a problem was introduced.
AJ