After upgrading the Bitbucket Server Integration plugin from 4.0.0 to 4.1.4, pull requests started to fail on Multibranch Pipeline jobs.

The error indicates that Jenkins cannot find the corresponding commit:

13:31:06  ERROR: Checkout failed
13:31:06  hudson.plugins.git.GitException: Command "git checkout -f b47595c059dfdd52e85ed638914892c06a9a425e" returned status code 128:
13:31:06  stdout: 
13:31:06  stderr: fatal: reference is not a tree: b47595c059dfdd52e85ed638914892c06a9a425e 

Reverting to Bitbucket Server Integration 4.0.0 resolves the problem.

I compared build logs from both versions of the plugin. When the older version (4.0.0) is used, the PR refspec gets added to the fetch command:

git fetch --no-tags --force --progress – REDACTED.git +refs/heads/:refs/remotes/origin/ +refs/pull-requests/39/from:refs/remotes/origin/PR-39 

However, this is not present with the newer version of the plugin:

git fetch --no-tags --force --progress – REDACTED.git +refs/heads/:refs/remotes/origin/ 

So the subsequent checkout cannot find the reference.