[x]):For some reason, a project with a recently merged PR (there are no more outstanding PRs) is showing a -1 in its count badge.

We have found the same issue here, our count is on -2, we've found out that 2 of our PR were closed twice, which should not even be possible. So it looks like a bug on closing PRs.
You are correct. I just merged a PR on another project and I can see the PR is closed twice, even though the merge operation only happened once:

I suspect this was recently introduced.
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We have found the same issue here, our count is on -2, we've found out that 2 of our PR were closed twice, which should not even be possible. So it looks like a bug on closing PRs.