My issue was different than the others above and I've run into it a couple times over the years. During CI automation we run fastlane and ran into this mysterious Command CodeSign failed with a nonzero exit code. Both times the fix was to manually start up Xcode start building and then there would be a CodeSign pop up asking for credentials. It only occurs when setting up a new machine.

@En-iNgo Did you ever get an update from Apple? I'm also running into this as of this week. It randomly started happening even though we've been on Xcode 16.2 for a while now.