Odd how fake bones can be the means through which miracles are wrought.
Actually, she was never in the General Calendar
From 1837 to 1961 celebration of her liturgical feast was approved for some places, but was never included in the General Roman Calendar for universal use. The 1920 typical edition of the Roman Missal included a mention of her, under 11 August, in the section headed Missae pro aliquibus locis (Masses for some places), with an indication that the Mass to be used in those places was one from the common of a Virgin Martyr, without any collect proper to the saint.
On 14 February 1961, the Holy See ordered that the name of Saint Philomena be removed from all liturgical calendars that mentioned her. Accordingly, the 1962 Roman Missal, the edition whose continued use as an extraordinary form of the Roman Rite is authorized by the motu proprio Summorum Pontificum, also has no mention of her.
As for the problems,
The Holy See's instruction to remove the name of Philomena even from local calendars followed the raising of questions by certain scholars, whose interest had been drawn to the phenomenon more especially in connection with the revelations of Sister Maria Luisa di Gesù. The questions were raised in particular by Orazio Marucchi, whose conclusions won the support of Johann Peter Kirsch, an archaeologist and ecclesiastical historian who is the author of the article on Philomena in the Catholic Encyclopedia, an article that has won the support of the historian William Carroll; but according to Mark Miravalle the conclusions have been rejected by others.http://en.wikipedia.org/wiki/St_philomena
The inscription on the three tiles that had provided the Latin name "Filumena" ("Philomena" in English) belonged to the middle or second half of the second century, while the body that had been found was of the fourth century, when the persecutions of Christians had ended. Not only the name but also the leaf, the two anchors and the palm that decorated the three tiles, and which had been believed to indicate that Filumena was a martyr (though the necessary connection between these symbols and martyrdom has been denied), had no relation to the person whose remains were found. The disarrangement of the tiles was something fourth-century sextons regularly did when re-using materials already engraved, with the aim of indicating that it was not the same person who was now buried in the place.
The rector of the shrine in Mugnano del Cardinale disputes these findings. After reporting the decision of the Sacred Congregation of Rites in 1961 as resulting from the studies of scholars, the Italian-language Enciclopedia dei Santi says that there still remain the miracles that occurred and the official recognition that the Church gave in the nineteenth century, the personal devotion to Saint Philomena of popes and people who were later canonized, and the widespread general devotion that still persists, particularly at Mugnano del Cardinale in the Diocese of Nola, where pilgrims from all over the world arrive continually, giving a display of intense popular devotion.
For many, the 1961 withdrawal of Pope Gregory XVI's 1837 authorization of liturgical veneration of Saint Philomena in a limited number of places (which was not an official declaration that she never existed nor that she is not a saint) merely means that the situation has returned to that existing before 1837, when in many places there was fervent devotion to her, accompanied only by vague speculation about the circumstances of her life and death or by belief in the revelations of the Neapolitan nun. The removal of an individual from the calendar does not necessarily indicate that he or she is not a saint.
We remain free to pray to her if we so wish. Those of us who do hold her to be a martyr of Diocletian's persecution. She was martyred at the age of thirteen.
(The entry on her in the Catholic Encyclopedia is particularly disappointing.)