Look beneath the leaf. This is usually caused by sucking insects such as white fly, spider mite. Sometimes the insect will poke their proboscis into the top of the leaf to insert eggs into the leaf. Please take a picture of the underside of the leaf. I'd nip those leaves off at the stem if there are only a few of them. Your plants are going to be producing peppers on a window sill? That is amazing. What is interesting is how insects got INTO your home to do this. Have you seen any flies?
You will also have to manually try to pollinate the flowers. Give them a good shake now and then or using a tiny paint brush get some pollen on your brush and swish it around on your flower. Have these plants been outside? I'd take them out and acclimate them to the out of doors...starting with 10 minutes for a couple of days, then 20 minutes for a couple of days and so on...to get them used to the sun. This thickens the epidermal cells so that they don't get sunburn. Insects outside will pollinate for sure and the sun will help your plants make enough food for energy to make better and more fruit.
They most certainly can stay in their pots. By the way, is this soil from your garden? If it isn't sterilized potting soil which I always use for any potted plant, that might be the reason for the insects. There are other options if we find that this is insect damage so please send another picture or two with more information...
The shriveling at the tips and margins is indicative of tap water use or too much fertilizer. Too high of salts.