Do Parathas, Naan, and Roti have to be burnt a little?
The charring is crucial to both the flavor and the texture. The charred part itself brings a bitter note to the flavor. If you don't like it, you can cut it out, but many people would miss it. It's also crunchy, which provides a pleasant contrast to the chewy parts of the bread.

It's also incidental to the way it's cooked. In order to get the flavorful Maillard reactions (the brown spots), you need to subject it to very high heat. Because you're cooking it without fat, some parts are closer to the pan than others. So some parts become brown, while other parts remain white, and a few spots become black.

Similarly, that high-heat cooking is important to the texture. It's what gives you a crispy outside without drying out the inside. If you cook thin breads like this at lower temperature, they will eventually become brown without burning, but they'll also become hard.

If you don't like it, discard it.