Github Organization Folder created jobs and folders that points to 404 url and wrong jobs.

We have a github organization: tsqe
In the org, there are couple repositories.

When using Github Organization folder with jenkinsfile from SCM, the generated repository folders has mismatched job for branches. see attachments

There are 4 repos under the org:, see tsqe-generated-repo-folders.PNG

• bbtf2
• bbtfmini
• cloudbee_sample
• tsfixsim

but within bbtf2, it has jobs created for

• >>bbtfmini>>master
• >>bbtfmini >> PR-222

These are just one example of this behavior. Because of these we are not able to reliably use pipeline scripts to provide CI on organization level

Please advise, Thanks