So in MCC I should have gotten the achievements for completing the Legendary campaign for Halo CE and Halo 2 and one Halo 4 mission “forerunner” and instead I get 1 mission that the game says I completed on legendary for Halo CE and 3 missions (also apparently “completed”) in Halo 2 with all having the same score time of 1 hr 49 min and 39 seconds? For some reason it has only affected these 3 games and not Halo 3? Why are these achievements not working??? Do I have to go through some of those hellish missions like the library again? PLEASE HELP HALO WAYPOINT PEOPLE!!! 
-Zilla 2K
I cannot deduce why halo Waypoint failed to track your progress, but try completing a level on legendary in coop and see if it picks that up. I am sorry, but you will have to redo the library again on legendary.