Since ballet flats need to fit snugly enough to not fall off your feet while walking, they may irritate the back of your heel if they don't fit perfectly. Of course, this has more to do with the shoes causing friction on your skin, which likely means they are an incorrect size. Using gel dots that stick to the inside of your shoes can help reduce some of that friction on your heels. 

Since ballet flats work best when it feels like they are "molded" to your exact foot shape, trying various sizes from different brands can also help you find the right fit for you. Some styles of flats have a narrow pointed toe for a sophisticated and elevated look. However, for those with wider feet, this shape can squish their toes and cut off circulation. This is one of the reasons why you never wear shoes that are too small. Understanding if you have narrow or wide feet can help you find styles that are a better fit. Some flats even specify "wide" in their sizing, making your search easier.