Oooo... not good! Something is not set up right. Try moving the sight frame up and moving the pins down within the sight frame. You don't want those arrows hitting anything as they leave the bow. If you look at a nocked arrow on the rest from the side of the bow is the arrow at the same height as the rest mount hole or is the shaft sitting above that hole. Your rest may be set too high up. (If you move it down you'll have to adjust the nock point on the string down equally.)

"it was only when I shot it though, when i had the arrow stationary there was more than enough clearance." This leads me to believe that the arrow is kicking nock high as it leaves the string. If you're shooting a release, try moving the nock point down the string until the arrow is nearly level (perpendicular to the string).