In The Girl Who Died we learn that Maisie Williams's character Ashildr is
This is referenced as part of a prophecy in The Witch's Apprentice but has it been an earlier prophecy or something that's just been created this season?
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All the previous references to hybrids are listed in this Wikia page. There have been several over the course of the show, most notably River Song, Donna Noble, and possibly - according to the Eighth - the Doctor himself. But the first reference to a Time Lord prophecy about hybrids was in Davros's taunt in Series 9 episode 2, The Witch's Familiar:
“There was a prophecy, Doctor, on your own world. It spoke of a hybrid creature. Two great warrior races forced together to create a warrior greater than either. Is that what you ran from Doctor, your part in the coming of the hybrid? Half Dalek, half Time Lord."
So no, it hasn't been referenced before. It seems to be a Series 9 thing, and may in fact be the main story arc of Series 9. See this quote from Steven Moffat in Doctor Who Magazine #492:
“We know the Doctor has done unmentioned – and unmentionable – things during the Time War. Even now that his biggest crime has been reversed. John Hurt seemed very young in The Night of the Doctor, but very old by The Day of the Doctor. What happened during those years? He clearly did a lot of bad things during the Time War. He was the most terrifying warrior. And that’s the thing we play with this year. What did he get up to in the years we didn’t see him?
He adds: “Now, having spent a lot of time writing the show, I think the character of the Doctor is actually quite well delineated. I get him. I get that he’s aspiring to be a thing called ‘the Doctor’, but he isn’t really. I get that he’s at some level an exceptional but nevertheless quite ordinary person, trying to live up to an impossible ideal. I think that’s all there. And so you have to wonder what fired him off Gallifrey in the first place…”
Asked specifically if it ties to the Hybrid, Moffat teases: “You’ll just have to keep watching, won’t you.”