If you save/quit a mission in Halo 3:ODST Xbox One edition, and then resume that mission and complete it, the mission registers that it is completed on Halo MCC however achievements fail to register that the mission is completed, as does Halo Waypoint.
So far I can only confirm this happens on Legendary.
EDIT: Here is my progress in ODST- if you scroll down you can see that I have found the clues for missions afterwards (through Achieve.ments> Halo 3:ODST) thus I have finished the missions and progressed past them.