Playing Multiplayer Destroys Progression

If I delete my save files and do my first game as multiplayer with someone who has already collected a collectible or destroyed a relay beacon, I will never be able to get those items or destroy those relay beacons in my own game. (Barring some relay beacons.) The same thing happens when creating multiple characters, though somewhat differently. Why??? I should still be able to do all the things if I play multiplayer with someones whos played before. Not sure if right topic to put under.