I also e-mailed FIFA about it and even tweeted to @fifamedia about it.
They've replied on Monday:
Thank you for your email and notification of a possible error in the World Ranking. We have reviewed the calculation and confirmed that there was a mistake. We will therefore issue a new ranking this week on fifa.com including the matches played on 19th and 20th August and also the two forfeit wins of Tadjikistan against Syria. Apologies for any inconvenience.
Communications & Public Affairs Division
FIFA – Fédération Internationale de Football Association www.FIFA.com
52 teams were affected. These are the changes (compared to the first September ranking):
33 - Tajikistan
7 - Lesotho
2 - Bahrain, Cuba and Iraq
1 - Azerbaijan, Saudi Arabia, Kuwait, Antigua and Barbuda, Oman, Iceland, Guatemala, Comoros, Kyrgyzstan and Solomon Islands
-8 - Syria
-4 - Dominican Republic
-3 - Qatar
-1 - Gambia, Faroe Islands, Tanzania, Liberia, Congo DR, Vietnam, Kenya, Kazakhstan, Ethiopia, Belize, Nepal, Burundi, Turkmenistan, Rwanda, Congo, Puerto Rico, Lebanon, Fiji, Malaysia, Dominica, Barbados, US Virgin Islands, Bahamas, Equatorial Guinea, Malta, New Caledonia, Hong Kong, Nicaragua, Chad, Palestine, Guinea-Bissau, India, Mongolia, Maldives and Philippines
133 - Tajikistan
9 - Lesotho
4 - Iraq
1 - Swaziland
-4 - Curaçao
-6 - Sudan
-7 - Dominican Republic
-10 - Qatar
-45 - Syria
That's why I posted a new preview and probable ranking for October.