Referring to the flag numbers here: http://www.assassinscreed-maps.com/Masyaf.htm Flag #6 is the most commonly missed because it's way off the map in an area you have no reason to visit after Memory Block 1 (and flags don't appear until MB2). Flag #18 is sometimes missed because there's another area nearby that looks similar. Flag #9 because, I don't know, some people always walk down the slope to the right.
If you get to 18 and can't find the last 2 they are probably the ones in the courtyard at the back of the assassins main building - that area doesn't unlock when the flags are first able to be collected, but unlock I think when you first return to Masyaf after completing the first proper assassination.
Use the assassins creed maps guide with the screenshots and checklist. They are all shown and are all in the game. Just make sure to exactly line up your screen with the screenshot to make sure you are in the right place.