Hello Karina,
I've seen something similar before. Did you delete it from the PFTC task view? I've noticed there are sometimes odd inconsistencies between the WS-task (main PFTC screen) and WS-template (WF builder) containers. Best approach is to always manage everything in the WF builder, that way I've never experienced any synchronisation issues.
Maybe add the affected container elements to the WF builder, save, activate. Go out, back in and delete from the WF builder. Or, failing that do the same but generate a new version after activating.
Regards,
Mike