These types of blemishes are often caused by water on the leaves and are generally harmless. Quite often the lowest leaves can touch the soil during the night when the plant lowers its leaves and this too can leave the same marks. They can also be caused by too much nutrition, especially nitrogen and to have deficiencies at this early stage and in fresh soil is highly unlikely. Flushing unnecessarily can do more harm than good, by leaching out valuable nutrients and "drowning" roots and is not the solution to every perceived problem, real or not.
Give your plants a chance to get established, at this early age and in new soil, they will not need feeding for some weeks yet. The best thing to give plants like this is a seaweed extract or tonic, it can not burn plants, but it will encourage roots to grow and increase plant vitality greatly. In fact, giving a seaweed extract every 2-3 weeks is highly beneficial, from seedling stage right through to nearly ready to harvest.
Hope this helps,..........
Organoman.