It seems like there might have been some kind of rights jockeying going on. It's not just QS being in two movies, but SW being left out of much of the early concept art for Civil War (to the point that some people were just expecting her to die too). Whether they've cleared this issue up or not, I don't know.
Quicksilver was announced for Days of Future Past after Marvel had already announced him for AoU, so I don't know what was going on there, except that both studios seemed to want to claim him and now Fox has him pretty much exclusively.
I think that the deal they made was for Disney to kill their version of Quicksilver and let Fox have exclusive use of their version. In exchange, Fox would never introduce their version of Scarlet Witch and let the Marvel one be the only one.