We are currently working on updating GADM to create version 3 which should become available later in 2015. Here are some known problems (and sometimes solutions) reported by GADM users.
There are now around 400 official districts in Afghanistan. There are also now 34 provinces (Daykundi, created from the northern part of Uruzgan, and Panjshir created from the northeastern part of Parwan or the northern part of Kapisa, depending on which sources you look at). There are also a number of unofficial districts and temporary districts; the situation there is constantly at flux, and the distinct borders are not available.
The partidos for Gran Buenos Aires (GBA) don't seem to match up completely with Census 2010 for Argentina. One example is partido Morón. It is broken into 3 partidos (Morón, Hurlingham, and Ituzaingó) on wikipedia and anywhere else I search for the GBA partidos. There are other examples too such as General Sarmiento being 3 partidos in other sources.
The data for Denmark is outdated. An administrative reform reduced the number of municipalitys to ca. 91 and the number of regions to five.
does not include the new district boundaries for Saxony-Anhalt.
Ghana now has 170 local government units (district assemblies) (GADM has the 137 old ones)
Haiti is missing two commune boundaries - Tabarre and Cite Soleil (Fixed in version 2.7)
Three powiats are missing: Wroclaw and Legnica (both situated in Lower Silesian) and Elblag (Warmian-Masurian). Here is a file with some remapping of names to make them the same as the ones used by Polish Statistical Office: http://img.grotos.net/pl_mapping.csv
Moscow should be separate from Moscow region in the R level 1 file. Apart from this, Perm' and Komi-Permyak were merged into Perm' kray, Taymyr and Evenk were merged with Krasnoyarsk (as noticed in the remarks), Kamchatka and Koryak were merged into Kamchatka kray, Ust-Orda Buryat was merged with Irkutsk, Chita and Aga Buryat were merged to form Zabaykalsky kray. (Fixed in version 2.7)
The Level 1 (prefecture) and Level 2 (Commune) boundaries that you use for Rwanda pre-date the major administrative reform initiated in 2002 and brought into effect from the beginning of 2006. There are now 5 provinces (Intara) and 30 districts (Akarere) replacing the 10 prefectures and 142 communes. The districts are further sub-divided into three more levels, for which I do not have maps yet. Maps of the new provincial and district boundaries can be obtained from CGIS in Butare, and downloaded from the GAUL website
GADM contains the boundaries of the magisterial districts which were in place in South Africa prior to the multiple rounds of local govt. redemarcation that took place after 1994. This is valuable -- itit makes it possible to compare stats which were collected for 100+ years on a magisterial district basis with more recent data. But for reference, current border data is available from http://www.demarcation.org.za/
Abyei between Sudan and South Sudan is not delineated.
The boundary between Tanzania and Burundi, in the area between Lakes Victoria and Tanganyika, has been set to the "official" boundary of Tanzania, and does not correspond with the boundary shown on Burundi maps. Tha GAUL admin boundary maps of Africa do not attempt to resolve this conflict, but show both boundaries. Admin boundaries for Tanzania on the shores of Lake Victoria attempt to follow the shorelines and numerous islands. They are grossly oversimplified, and often innaccurate as compared to satellite imagery or to the SRTM-derived swb maps. Some other countries around this lake (eg Uganda) avoid this problem by using offshore linear boundaries, so that all islands within these polygons are assigned to a single administrative unit.
2 Uzbekistan territories inside Kyrgyzstan are missing