She only has to make up the day that she did not fast in Ramadaan, because the day she was fasting when her period came was only to replace the day that she did not fast in Ramadaan; it was not a new obligatory fast.
Ibn Hazm said in al-Muhalla (6/271): Whoever deliberately breaks a fast observed to make up for a missed Ramadaan fast only has to make up one day, because the obligation to make up the fast applies only to the Ramadaan fast. It was narrated in a saheeh report that the Prophet (peace and blessings of Allaah be upon him) made up that day he missed of Ramadaan. So it is not permissible to add more to it without any shar'i text to support that and without any scholarly consensus. It was narrated from one of the salaf that he has to make up two days, the day from Ramadaan and the day when he was making up that fast.
It says in al-Taaj wa'l-Ikleel: Whoever breaks a fast observed to make up for a missed day from Ramadaan only has to make up one day. 3/387.
And Allaah knows best.
Reproduced from Islam QA