In current release version prune works after fetch. (yeah, I saw this bugfix https://issues.jenkins-ci.org/browse/JENKINS-10348)

But here the bad situation:
1) Create "abc" branch in git repo.
2) Build this branch by Jenkins.
3) Abandon commit and delete branch.
4) Create "abc/asd" branch, trying to build it... and we got a problem.

UPD: my bad, now I see what happens with Prune in refactoring branch. But the problem is still there - Prune executes after fetch, not before it.