Kamil Kopaczyk Please open a new issue since this issue is 5 years old and in the new issue try to specify as much as possible what version of Jenkins and plugins you are using. 

Does anybody know what is the recommended solution for fixing this? Jenkins does not allow me to downgrade jquery plugins, since they are used by other dependencies.

Did anybody managed to find out what causes this issue? Which rules or which change in scripts exactly causes this?

Patrik Boström maybe it's worth to reopen this as a sign, that is still a known issue and currently there's no reasonable solution?

Hello to all.

What is the "correct" workaround to this issue.

We also not remove or downgrade the plugin because of others dependencies...

boaz shavit, the formatting in Laurent Gillet's comment is broken. Comment with corrected formatting:

An easy workaround consists in modifying pipeline-common.css (in theme) as follow:

Original value:

._jsPlumb_connector {
    z-index: -100;
}

New value:

._jsPlumb_connector {
    z-index: 0;
}

However, that workaround doesn't work for me.

It looks like the Original value and the new value are the same.
I'm having the same issue where the arrows are not showing and adding the Unknown macro:

to pipeline-common.css did not solve the issue.