I am not sure I would call water going through a designed hole a leak. That's like saying a glass leaks out the top. They are great mats but are only designed to hold so much water. If you really wanted to close that hole up you might be able to use something like a inner tube repair kit and just glue a small piece of rubber over the opening.
2013 JKU True Blue, 4" Zone Lift, 35x12.5x17 Nitto Trail Grapplers, ION 171 Black and Machined Wheels