Thanks Ray,
I see the behavior rewrote my manually created filter by creating a new second filter
$DeleteQuery->Action = "delete";
$DeleteQuery->Table = "projects_companies_assigned";
$DeleteQuery->addFilter("psaProject", "=", "i", "".$projectTarget ."");
$DeleteQuery->addFilter("psaType", "=", "i", "".$companyType ."", "AND ", "psaProject", "=", "".$projectTarget ."");
$DeleteQuery->execute();
That explains why it was working. I did not see the additional line originally.