Careless handling by people (from all walks of life) could be the is main cause. Also some bank employee and employees of other institutions which handle the large amount notes write on the notes using pen. Sometime they staple the notes. Yesterday, I actually saw Life Insurance Corporation of India (LIC) employee writing the total sum on the top note. I hope she listens to RBI's following policy guideline (issued in 2007) about handling notes.
"It has, therefore, been decided that hereinafter and with immediate effect :
a. banks should do away with stapling of any note packets and instead secure them with paper bands,
b. banks should sort notes into re-issuables and non-issuables, and issue only clean notes to public. Soiled notes in unstapled condition may be tendered at the Reserve Bank in inward remittances through Currency Chests; and,
c. banks should forthwith stop writing of any kind on watermark window of bank notes."
Although policy is for banks, it would be nice if LIC being so big and pervasive thought out India, follows it, not out of compulsion, but to keep the notes clean and increase their life span.
As per this FAQ on RBI website, all banks should accept partially damaned notes, so if you have them just submit at your nearest bank.
BTW did you know about RBI's Project Financial Literacy. It is available in many regional languages, well done RBI.