Nutrient deficiency is obviously the reason. At acclimatization stage you can wet your cloned plants with a very dilute MS medium 1/10 to prevent such occurrences as you are experiencing with your plant and you may withdraw wetting as soon as they get acclimatized. You can also do as suggested by Rajesh Kondamudi.
How long did it last? I had noticed same kind o spots on wheat plants in the field in a same position and all plants from one germplasm. I took it as a "marker", not a problem.