In testing upgrading the Jenkins core and plugins I've encountered this twice; last time was about a year ago and I was able to resolve it by reverting the git plugin to 4.3.0 and Bitbucket pullrequest builder plugin to 1.4.28

When jobs are triggered with the Bitbucket Pullrequest Builder Plugin, the git clone uses the latest commit on the target branch, not the HEAD of the dev branch being tested. That commit is visible in the console output but it reports an error stating the commit is from a different repo:

The pull request:

And the git info summary on the CI job lists the target branch, not the source branch, as is the case with pre-upgrade jobs:

I confirmed same results with pipeline and freestyle jobs.