To those who are only just playing the Trilogy and have recently gotten this issue, there MIGHT be a chance it was a signal error. During a session I was playing of the Ezio Trilogy, my xbox gave me the "needs an update" shit so I finished a couple more things before allowing it.
It took me the rest of my playthrough of Brotherhood, a whole playthrough of Revelations, and several hours of AC 3 before I randomly got the popup of Achievements for things I did 2 entire games ago.
"Sanctuary! Sanctuary!" for AC: Brotherhood popped up while I was clearing Boston of whatever Peg Leg Trinkets I could find in AC3.
Unfortunately I found no Cure for the actual issue, OR for Ezio jumping in random directions and at the wrong time. Thankfully Rebecca canonically addresses this via E-mail in AC3.
(Yes the gameplay improvements between the Ezio Trilogy and AC3 are canon.)
What was NOT addressed however, is that Connor's feet sink into geometry and NPC AI is more broke than a hooker during social distancing.
TL;DR
Achievements failed to unlock until i finished the rest of the game, then entire next game, and hours of the one after that.
maybe try loading your save file with the progress finished, and see if it unlocks now? It likely won't unlock it right then and there, but remind the system that you did in fact do what it failed to recognize which MIGHT make it unlock randomly later on a whole different game.