Are there any ways to fix the disappearing flags bug in Assassin's Creed?

Solution 1:

Do you know which flag you didn't get credit for? If the game thinks that you don't have it, then you might be able to pick it up again if you leave the town and come back.

However, if the game knows that you have picked it up, but it hasn't given you credit for it somewhere else, then there's probably nothing you can do to fix it.

Solution 2:

Just leave the area and come back and retrieve the flag again. If that doesn't work, I'm not sure of what you can do.

Solution 3:

Sounds like you (and your friend) may have just missed one. This has happened to me in a few other games. Just make sure that you save every time you quit, and never mark a flag as "found" until you physically pick it up.