Small very soft towels or other fabric
Cut the towel into two stripes with the length covering the uncomfortable area of the shoe. Match them against the shoe and adjust the shape to fit inside the shoe. Since edges of the shoes tend to be quite sharp, I prefer to leave the liners a bit wider so that they cover the edge as well. It doesn't look that pretty but I'd rather have the shoes less cute in the back than my feet bleeding daily.
Glue double-sided tape on the back of the liner.
Glue inside the shoes! Super easy, cheap, easily replacable and comfortable. ^^~