Only American 7th Army and French 1st Armies staged through Marseilles. I think you are confusing 7th with 9th. If you look back at this German map from July 9, 1944, you can see where they identified the HQ of 9th Army still in England near Oxford.
Ninth Army entered the continent and was activated after 3rd Army had raced off to the east south of Paris. Since 3rd Army VIII Corps had been tasked with the reduction of the French port of Brest, and most of it's lead elements were racing toward Lorraine hundreds of miles away, 9th Army was activated, and took over command of VII Corps for the task of the reduction of Brest.
After that port fell, 9th Army was inserted between US 1st Army and British 2nd Army in October. It first starts showing up on German intelligence maps in early November, but they think it is in the Ardennes.
When 12th Army Group launches Operation Queen to clear the area between Aachen and the Rhine, and on their map of November 21, the Germans do know where it is.
