I used http://www.assassinscreed-maps.com/ to track each flag as I found them. I still had 1 flag left when it was all over.
I heard that there was 1 glitchy flag that sometimes disappear/reappear for no reason. I played the game on/off for a week just trying to get that last flag to hopefully reappear, but it never did.
It's a conspiracy, I tell you - To glitch or not to glitch...
Q. I can’t find Flag/Templar number X, is this a glitch?
A. While glitches do happen all too often in this game,
not being able to find a Flag/Templar is often not a glitch. Before deciding that you have a glitch, you should go through each Flag/Templar in order making sure to line up your screen exactly with the picture on the map. More often than not, people find that they were in the wrong place and marked of a Flag/Templar that they have not collected.
Q. I’ve gone through the maps several times and I still can’t find the one that I missed. HELP!!!
A.
Try resetting your system or clearing the system cache. Often doing so will make a glitched Flag/Templar suddenly spawn.