We are seeing duplicate builds triggered on Jenkins multibranch pipeline projects. Builds are normally triggered using push notifications from Bitbucket using this plugin: http
You can add property "Supress Automatic SCM Trigger" to job configuration:
Supress Automatic SCM Trigger Property
This will prevent builds to execute due to "Branch Indexing".
The downside is that you may need to manually trigger the branch specific build at least once to get the configuration applied from Jenkinsfile.