When pull requests are configured to use "Merging the pull request with the current target branch revision" there's a full branch checkout into a @script directory that is merged with the target branch whenever a PR's target branch changes. These directories aren't removed when the build finishes.

This was earlier reported in github (https://github.com/jenkinsci/bitbucket-branch-source-plugin/issues/847) and there it was suggested to enable "Prune stale remote-tracking branches" and "Check out to matching local branch", but this doesn't make any difference for me.

The github issue was closed because there was no response from the issue reporter (not me).