The explanation for two awards is the fairly unique arrangement of the order of battle for the Marines in the AEF. Kelly was a Marine, in the USMC brigade of the AEF (4th Brigade, composed of the 5th and 6th Marines) that was actually part of a US Army Division (the 2nd Division, which included the 4th Marines, as well as the 3rd Brigade [9th and 23rd Infantry], 2nd Artillery, and Army divisional elements), in turn commanded by a Marine (Lejuene). The Marine Corps was simply too small for truly independent operations at that point, so this was how they were put into battle in France. Early on, even, Army officers were assigned to the Corps temporarily due to a lack of enough Marine officers when the Corps grew in size.

Anyways, Kelly earned his Medals at the Battle of Blanc Mont Ridge. The assault at Blanc Mont, considered near impossible by the French as it was against a particularly strong point in the line, succeeded masterfully and is considered the best action by the division in the war, and again, it was thoroughly a joint operation between the Corps and the Army. You will notice that there have been five awardees of the MOH for the same action, and all were Marines within the 2nd Division during WWI:

• Gunnery Sgt. Charles F. Homan
• Sgt. Louis Cukela
• Sgt. Matej Kocak
• Pvt. John Joseph Kelly
• Cpl. John Henry Pruitt

Although not all at Blanc Mont Ridge, in any case though, they all earned it for the same reason as above, namely the involvement in close cooperation of joint action with the Army, which was recognized by both their parent branch of the service (Marines->Navy), as well as the Army under whose umbrella they were operating at the time.

• The AEF Way of War: The American Army and Combat in World War I by Mark Ethan Grotelueschen
• America’s Heroes: Medal of Honor Recipients from the Civil War to Afghanistan by James H. Willbanks
• US Marine Corps in World War I 1917-1918 by Mark R. Henry