personally never had any experience with said "glitch," the only reason i never got around to doing these flags is because of how many there were. usually im the type of gamer who doesn't mind collectables too
just recently getting back into AC and i found it easy to get these, only need the middle district of Jerusalem now. i have just been collecting flags as i unlock the area, first viewpoints / citizens / investigation / flags, then i go to the bureau and start the assassination. i just found it easier to navigate with less clutter on the mini map.