Talk with the ballet instructor and point out what you are noticing. He or she may not be aware of your daughter's symptoms. A medical evaluation may be needed to rule out a true, anatomical problem.
Dancers are at risk for all kinds of problems just based on the extreme motions the joint goes through. For example, a dancer with a high arch has the perfect looking ankle by dancing standards. But in this position, the bones are shifted putting stress on the joint and ligaments.
Cracking or popping sounds and ankle locking are a sure sign that a exam is in order. Pain that doesn't go away with rest is also a red flag.