I just checked my rosemary plants (I have about 50) and none of them showed the brown markings on the leaves. Rosemary is one of the toughest plants there is apart from cacti, so I doubt it is a disease, but could be related to your being too kind to it. This plant is designed to live a tough life, surviving drought and poor nutrition and go on to produce very fragrant leaves. My experience has shown you can strike cuttings very easily in peaty potting soils, but as soon as possible move to regular non-improved garden soil and then never fertilize. Just keep moving to larger pots as you need it bigger.
If you are looking for a theory of the brown spots it might be because a surplus of one nutrient might be locking up a different nutrient and preventing assimilation by the roots.