Joan of Arc was burned as a heretic. Now she is a saint. How does the Roman Catholic Church explain this? It turned out that the Roman Catholic Church has murdered its own saint? Has any logical explanation ever been offered for this?
She was burned by the English clergy who denied her appeal to the Pope near the end of the Hundred Years War and she was cleared of all charges only 30 years after her death (even though it took almost 500 years to canonize her).
And yeah, there's been extensive research and analysis of what happened. The trial and the aftermath is all amazingly well documented and worth reading; or if you prefer historical fiction Mark Twain has an awesome book about her.
I'm no defender of the Roman Church, but if the Church is identified with Israel (which it is, the New Israel) it follows that it will be the one who kills the prophets, and then afterwards repents. I don't know how the Roman Church explains it given the particular theology surrounding the papacy, but in general the persons in the church from layman to highest bishop are all fallible.
In the history of the Church there have been good and bad leaders, and there have been saints who misunderstood and disliked each other (Cyril of Alexandria and John Chrysostom are a commonly-cited example.) In Athanasius' time, Athanasius was exiled and hounded countless times by the Church, but not because the Church was rejecting him, but because the leadership and others were fallible and didn't really understand what they were doing (to borrow Christ's words.)
Plus if I recall, the effects of Arius on the leaders there. He who 'deceived even the elect, if such a thing were possible.'