Discovered Pull Requests are not merged against target branch when being built, which is a problem because the Discovered Build result might change after the PR has been merged. Instead, the plugin should do a merge between source-branch against target-branch as the Pull Request indicates.

This can become a problem if target branch is more updated than source branch and the source branch might introduce incompatible changes with the updated changes in the target branch.

This behaviour is also how the Bitbucket Branch Source does it which is the one I consider correct.

Workaround: update the source-branch with the changes in the target-branch. However, this would be unnecessary if Jenkins does it for you which prevents issues.