It sounds like it may be leaf miner. They're the larvae of a small moth which burrows under the 'skin' of the leaf. You may see some if you look closely.
They can be warded off by using whiteoil on the leaves, don't do this in the hot sun or the leaves will burn.
These critters don't actually cause much harm to the host plant as it's only leaves they affect, so you can do nothing if you don't mind a few squiggly leaves.
Ensure your tomatoes and peppers get a side dressing of potassium, this'll toughen the leaves up a bit and also help with flowering and fruit formation.

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The secret is the soil.