The only explanation that makes sense is that she used up the stone before completing the process of bringing her brother back.
From the FMA Wikia:
Due to the absolute law of alchemy being equivalent exchange, the stone gives the illusion that someone is able to override that law. Being that it is an illusion, the powers of the stone itself are not unlimited, and only appears to allow an alchemist to bypass equivalent exchange as long as the stone retains its power.
From what can be seen in the movie, virtually as soon as she finishes, she coughs the stone back up and the stone disintegrates. Throughout the show, the stone disintegrating is used as a sign that the stone has run out of power (like with Father Cornelio's stone in the early episodes). This means that the stone ran out of power no later than her finishing her process. It would be incredibly improbably that it would run out perfectly when she finished, especially given the amount of power that she used previously, so that most logical explanation is that she ran out partway through and paid with her leg for the rest.
This is never explained in the movie, so this is only an educated guess based on information from the show and from the movie.