I tried reproducing it just by now and had no issues,
I have my main repo at my personal account then forked it at my own organization, created a pull request, then updated it, and it’s included at the pull request which was created prior to the update,
just make sure that the branch you used to create the pull request is the same branch you are updating,
or else, yup, if that seems to be a problem, you can always contact them,
Nope! This is weird and probably going to be hell for GitHub to debug. I don’t see anything suspicious in common with our two pull requests. Thanks for filing the issue.