This trophy is glitched in several ways. I'll list the ones I know about and what I did to overcome them. I had to play through the entire game 2 times since I got unlucky with the recruit completion glitch and was 10 points from 100% with no way to increase.
If You have the Perfectionist trophy then you are half there, finishing all story missions and optional objectives. The side missions and other challenges are the most likely to glitch.
1. Assassin recruit glitch: This one is annoying and the reason I am making this guide. I have found many forum posts and questions about this glitch with no actual answers. In short you can max level your recruits to level 11 but their completion in the synch tracker will show less then 100%. Any of the recruits can glitch from what I gather. My way around it that will hopefully work is this. Play through the game normally, I completed all side quests as they became available to have them out of the way. There is a glitch with the Frontier side quest "UFO" so make sure you finish it soon after arriving in Boston. I unlocked all 3 recruits in Boston but didn't start to level them up at all. After you finish chapter 9 you will be able to get the recruits in New York. As far as I can tell talking to the recruits for optional conversations in taverns does nothing for their completion. Calling them in and using their abilities (Lure, bodyguard etc.) also doesn't seem to matter. Only earning exp and leveling to 11 matters on their completion. Since the recruit that glitched was from NY I made a backup save before actually liberating NY and getting the recruits. I then got the last 3 and began sending them on missions to earn XP. You can call them for aid and get them to earn XP that way but this worked for me. While they were on missions I stopped with the story and found collectibles, finished side missions, homestead missions, frontier, hunting etc. Do anything to pass the time. I don't know if it makes a difference but when the mission was over I didn't skip the message on the mission screen about who was back and what they earned. I did it this way so that if someone glitched I would be able to revert my save and try again. Luckily no one did the 2nd time around.
2. UFO glitch: As mentioned above the Frontier sidequest UFO in Boston can glitch if it becomes available but isn't completed before moving forward at a certain point. I have found many forum posts about it and the consensus is to complete it and the other side missions found in Boston as soon as you have access to them.
3. George Washington speeches: One of the frontier objectives is to listen to all of GW speeches. The first 2 are on the Ch. 9.1 mission, you go to Valley Forge camp and meet GW there. After he gives you the mission instead of going forward with it check the map for a 'W' and run there. Speak to GW and let the speech play out, you can press O and skip it but talking to him again just began the same speech instead of the next one. After speech 1 is finished the GW will be a short distance away, run to him and do the same thing. This time you will follow him as he walks around and talks to you instead of a cutscene speech. After this you cannot speak to him for the last speech until you have finished the story, GW will be in NY at the SW of the map. go there and speak with him again for the final speech.
Civilian missions: Not really a glitch but there are a lot of questions about them. The delivery missions do not add completion to your tracker as you complete them. Only when you have done all of them in Boston, NY and the frontier do they show as complete. So it will increase in 33% increments until all deliveries are finished. One thing that gave me trouble with the deliveries is that it almost seems like you can only have one delivery mission per area at a time. If you find the delivery request but interacting with the quest giver doesn't work make sure you have finished any delivery in the same city as the one you are trying to get. I did have to finish a delivery in NY, quit to main menu and then re-enter the game before the giver actually began the delivery mission I was then able to give him the items with no issue. The thief club is unlocked by pickpocketing people until you have stolen around 200 pounds.
https://www.ign.com/wikis/assassins-creed-3/ has all the locations of side missions and tips for finishing optional objectives. I hope someone is able to use this to save some head and heartache. Good luck and happy hunting.