When using pull requests with merge strategy Squash Source Branch Commits all commits are squashed and the new commit is build from the PR title + description.

If the pull request source branch had multiple commits and one of them had a message fixes issue #123 then this source branch commit is linked with the issue as fixing commit once the PR is merged. IMHO it should only link the new squashed commit instead because the commit on the pull request source branch will not exist in the repo after PR has been merged. Of course the squashed commit should only be linked to the issue if the PR title or description contains fixes issue #123.

This would also be consistent with issue transitions as they react on the title + description of the squashed commit and not on the PR's source branch commits.