Could be a number of things. Does she get the pain under her foot while running? If so, it could be plantar fascitis.
Get her to roll her feet (one at a time - under the arch) around on tennis ball - 10 mins each leg every day for 2 weeks. Should know in a few days whether it heps or not.
Or if it is only bothering her in the stretch - then.....dont do the stretch anymore!!