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It sounds like you have aIt sounds like you have a problem with leaf miners. The larvae will tunnel through the leaves and stunt the growth of your plant. Leaf miners are difficult to control without using insecticides. The adult leaf miner flies can be attracted by yellow cards coated with a sticky layer of petroleum jelly. Keep your plants healthy and well watered and they may recover from the infestation. Tomato plants need a lot of sun. If possible move your container to a location where it will get more morning sun.

2015 Special Edition Garden GuideCooking Fresh with The Old Farmer's AlmanacThe Almanac Monthly Digital MagazineWhat the heck is a Garden Hod?