Edema, probably from overwatering.

Those are eggs from a Ugandan Tiger Worm. Once they hatch, the larva will drop to the soil and burrow down and consume the root system of your peppers. The only effective treatment is military grade Napalm. But, they could also be Edema as well. Skip the Napalm in that case.

I have two plants grown from seeds of Jalapeno peppers I bought at the grocery. Of all my overwintered pepper plants, they were the ones that suffered the worse case of edema when I might have over watered a bit. Maybe these are more fragile to it? It was way worse than your case. The affected leaves will eventually either heal and get a bit brittle, or dry up and fall. The plant should bounce back if not severe. Just check your watering schedule, and drainage of both potting mix and container.

Thanks all, I did have a chuckle when I read your comment esox! I will scale back the watering for the Jalapenos and hopefully all will be ok.