Academic effectiveness of universities is measured with the number of publications and citations. However, accessing all the publications of a university reveals a challenge related to the mistakes and standardization problems in citation indexes. The main aim of this study is to seek a solution for the unstandardized addresses and publication loss of universities with regard to this problem. To achieve this, all Turkey-addressed publications published between 1928 and 2009 were analyzed and evaluated deeply. The results show that the main mistakes are based on character or spelling, indexing and translation errors. Mentioned errors effect international visibility of universities negatively, make bibliometric studies based on affiliations unreliable and reveal incorrect university rankings. To inhibit these negative effects, an algorithm was created with finite state technique by using Nooj Transducer. Frequently used 47 different affiliation variations for Hacettepe University apart from "Hacettepe Univ" and "Univ Hacettepe" were determined by the help of finite state grammar graphs. In conclusion, this study presents some reasons of the inconsistencies for university rankings. It is suggested that, mistakes and standardization issues should be considered by librarians, authors, editors, policy makers and managers to be able to solve these problems.