Depending on the depth of the hole, this could cause a variety of problems in the future.
For some older roofing materials, it is a good idea to reinforce the surface with butyl tape and polyester fabric.

EPDM rubber is also often the main substance used in the weather seals of vehicles, such as door seals, window seals, and hood seals. This is due to the great weatherproof properties of this type of rubber.

EPDM sheeting is often used as a liner for back yard water ponds and other man-made water features. The rubber does not leach chemicals, and so would not harm any fish living in these ponds.