Ref T13130. See https://discourse.phabricator-community.org/t/unable-to-create-owners-package-with-same-path-in-multiple-repositories/1400/1.
When you edit paths in Owners, we deduplicate similar paths, like /x/y and /x/y/. However, this logic currently only examines the paths, and incorrectly deduplicates the same path in different repositories.
Instead, consider the repository before deduplicating.