Been fighting this one and just discovered the "Use field values for reference lookup" toggle that appears on the Action Item when Type is Script. Toggling this ON, displays a Set field values section below the Execution script.
Here, simply map the field your reference depends on.
In my case, I needed to filter Contacts based on the selected Account. Then I just set Accout > {{Input:i_account}} 

Hope that helps others bumping into this-