My 3 and a half year old son has a very similar problem! It's not every night, maybe 2 times a week. He complains about pain in his toes. Sometimes happens during the day. Or he will wake up in the middle of the night crying and kicking, stretching his legs and flexing his toes. His pediatrician told me the same thing - that it's normal. But from my research - growing pains are in the legs, not in toes.. so i'm planning to take him to pediatric podiatrist. Haven't found one yet.
For now i give him a little tylenol and rubbing/massaging helps sometimes.
I would ask to see a podiatrist.. take her to see that specialist and see what they say. The condition of Kohler's disease comes to mind, but this isn't a diagnosis. She needs to be seen by the specialist. good luck.