Dont think its a big problem as long as you check the car history and background from the concerned departments. Also you can check that the if the car is in the persons name you are purchasing it from at the excise department and look at the original file.
Main reason they are cheaper is because the dealers started this ''drama'' that because of only duplicate copy available the price shpuld be decreased, otherwise no such reason to.
Also agree with @mani1 that if cars have been involved in some crime then it could be a headache unless you get it verified, which means you cant be hassled and you get the car cheaper then usual.