The hyponychium, which is located under the distal end of your nail bed near your fingertip, is the reason for the pain when the nails are cut a little too short. It serves as a barrier to prevent debris and germs from making their way under the nails and also contains white blood cells to help fight infections. Cutting the nails too short exposes this barrier making your fingertips painful, sensitive, and irritated due to the nerve endings being exposed to pressure and the sensations it's normally protected from by the actual fingernail.