Heat a nonstick skillet over medium heat. Cook the zucchini, yellow squash, tomatoes, potatoes, and chile peppers, stirring occasionally, until the vegetables are tender, about 20 minutes. Transfer the vegetables to a bowl and set aside.
Return the skillet to the burner over medium heat. Crack the eggs into the skillet and fry them until the whites are set but the yolk is still runny, about 5 minutes. Add the eggs to the bowl of vegetables and season with salt and pepper.
Using two knives, cut into the eggs and vegetables, mincing the mixture up into small pieces until well blended. It will look mushy.
In a separate bowl, mix the harissa with water, one teaspoon at a time, until the mixture is pourable but still thick. Pour the harissa over the kaftaji and serve.