A phantom set element is there syntactically but it does not exist. This was used in the past to define an empty parameter statement. For example:

 
$phantom empty
parameter x / empty.empty 0 /

Nowadays one should use the $onompty dollar control option:

 
$onempty
parameter x(*,*) /  /;

The warning indicates that in there is a phantom set element empty in the workfile, which does not really exist.