To re-produce the issue is quite easy:
1. Create a workflow job with Definition Workflow script from SCM (with for example firstname.lastname@example.org:<ACCOUNT>/git-bitbucket.git) and then you specify a script Path flow-ci-dev.groovy with:
git credentialsId: '', url: 'email@example.com:<ACCOUNT>/git-bitbucket.git'
2. Click to build the job
You will see duplicated changes like the ones attached.
Not sure if this is a duplicate of JENKINS-29326 or if the issue is in Workflow or the git-plugin directly.