Hello guys, this is Yegues from Zauce Industries (http://www.youtube.com/zauceindustries
For those that are going to start playing this game for the first time, or want to go back and 100% it before ACIII comes out, you need to be aware of this.
I am sure many of you are aware of the fact that randomly a flag or templar will not count. This happened to me with one of the Jerusalem flags. People say leave the area immediately but that won't always work, and you can't reload because the game auto saves so frequently.
This is how to easily deal with this achievement, with this method, I basically did 3 play-throughs within 2 days without even doing too much work:
1. If this isn't your first time playing, ie. you're only really going for the collectible achievements and some random stuff, then simply play through the game while you have a map up with all the locations. Use a paint program to white out everything you've done (use a different color for flags and templars)
2. You ONLY need to do the very minimum. Each district only requires 2-3 investigations to move to the assassination. So only do that. Get the viewpoints only since you need to know where flags are.
3. Just go through the game until you get to the flag/templar that doesn't count. No matter where it is, immediately stop collecting from that district, or entire town unless it's one of the Acre districts since they have separate achievements.
4. Beat the game and get any other achievement you need.
5. Start a new playthrough, you don't need to finish the game unless it's for another achievement.
6. Go even less stuff than before. Only do the required investigations, not even viewpoints. You can rush through a district in like 10 minutes if you know the cities. DO NOT COLLECT/KILL ANY FLAG/TEMPLAR THAT YOU ALREADY HAVE THE ACHIEVEMENT FOR!!!!!!!!! Only collecting what you need will give you more chances that you won't have that bugged again.
7. Go through until you get to the district/town that you need and do viewpoints and get the flags, do the minimum amount of investigations and move on until you get the achievement you missed before.
The reasoning behind this as far as I understand is that between all of the flags and templars, there will randomly be 1 that is bugged. It is entirely random and cannot easily be fixed.