Why doesn't Jenkins lightweight checkout work- pipeline job

Question

Lightweight repository checkout is turned on in configuration, however it does nothing, job copies to Jenkins workspace not once but two times same repository (repository of Jenkinsfile). It should just use Jenkinsfile. I use other repositories in the pipeline job but there are none left in the Jenkins workspace which is good thing. I don’t know what settings in Jenkinsfile bother him. I can't conclude anything in the Console output log, it doesn't make any mistakes. Do you have any idea what might be bothering him? Some plugin? I use slave where I run jobs in the Docker container. This workspace where I have the unnecessary repository is on the master.