I looked for a NDS photo and found the one shown below. The clearance from the crank arm to the frame looks quite tight like yours, but I would still have a knowledgeable tech. check that your bike was assembled correctly.

Also, as shown in the bottom photo, you could install a bottle rack on the underside of the downtube with bottle or an improvised deflector to keep stones from the front wheel from reaching the area of the crank arm.