I made the relevant GitHub project public. You can find it here: https://github.com/marcoconnor-radio/GitHub-vs-Xcode

It has resolved itself on my side. I think one problem was a bunch of UTF-16 coded files (Localizable.strings) which should have been UTF-8. After closing the PR on GitHub, new PRs were working again. Could be a coincidence though :). It was on a different project on the same account.