We are currently working on updating GADM to create version 3 which should become available in early 2016. Here are some known problems 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.
Ghana now has 170 local government units (district assemblies) (GADM has the 137 old ones)
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
Abyei between Sudan and South Sudan is not delineated.
2 Uzbekistan territories inside Kyrgyzstan are missing