I tried to 100% Black Flag on X1 a few years ago. Something on it glitched to where I could only get 99%. Forget what it was now, but a known glitch apparently.
I registered a couple days ago just to reply to this... Hi people! I had to "get" the free Season 2 Prologue from the store and download it before the legacy pack would unlock for me. Not sure if the same issue for you.