These issue is related to following elements of PicketLink Federation Subsystem:
<service-providers>, <trust>, <handlers>, <keys>

All of these elements have no attributes and they are added automatically when their child element is added via CLI. It is correct behavior - according to XSD (wildfly-picketlink-federation_1_1.xsd), when any of these elements exists they have to contain at least one child element. However, when their last child element is removed, they stay written empty in configuration, which is not valid XML state according to XSD (e.g. <service-providers/> left in configuration).

These empty elements should be removed, when their last child element is removed or XSD should be updated to allow minOccurs="0" for their child elements.