We noticed that SpotBugs started using wrong reference builds. After further investigation we found out that the referenceJobName input field was missing on the project configuration page thus deleting the setting when the configuration is saved.

The only workaround for now is to manually edit the project config.xml and adding the following line:

<io.jenkins.plugins.analysis.core.steps.IssuesRecorder plugin="warnings-ng@8.9.1">
...
...
<referenceJobName>ReferenceJobName</referenceJobName>
...
...
</io.jenkins.plugins.analysis.core.steps.IssuesRecorder>