Indeed I had the same issue retrieving system administrator xml file via ANT.
You should mention "Admin" as profile name. your package.xml must be as followed :
<?xml version="1.0" encoding="UTF-8"?>
<Package xmlns="http://soap.sforce.com/2006/04/metadata">
<types>
<members>Location_Contact__c</members>
<name>CustomObject</name>
</types>
<types>
<members>Location_Contact__c-FSM Location Contact Layout</members>
<name>Layout</name>
</types>
<types>
<members>Admin</members>
<name>Profile</name>
</types>
<version>39.0</version>
</Package>
-
-
Location_Contact__c
CustomObject
-
Location_Contact__c-FSM Location Contact Layout
Layout
-
Admin
Profile
39.0