I came across this paper and the following discussion on the Partition of India. It is a fascinating paper, written by a famous professional geographer, Oskar Spate. He served on the Punjab Boundary Commission and there are quite a lot of interesting points which I found in his paper. (I learnt quite a lot about how canals, water ways, irrigation works, train lines, etc. form frontiers and how geography drives the country's frontiers!)
1. Khulna: I never knew that there was such a problem with respect to Khulna district. This is where my grandma comes from actually. But very interesting debate and discussion over which bits will go to which Dominion. I always knew that there was a problem and there was big issues on the west of the country, but never knew the challenges to the East. Apparently, the situations were reversed. The Sikhs and Congress wanted the division in the West to be done on the basis of economic, religious places and historical land ownership basis and the Muslims on the basis of population, while it was rather reversed in Bengal. Also, the chicken neck connecting Assam/rest of NE India to India is questionable to Oskar.
2. Gurdaspur: This district seems to be deep in the psyche of Pakistani's. I have to admit I never knew about this problem before. The problem was simple, it was majority Muslim and was still granted to India, the reverse to that of Khulna (not that that is mentioned by the Pakistani's! :)). To top it all, this was the heartland of the Qadiani's in the town of Qadian in the district of Gurdaspur. The link of this district to the retention of Jammu and Kashmir is also interesting (see the Wikipedia article on Gurdaspur)
3. Ahmadi/Qaidani's: These chaps seriously wanted to be part of Pakistan and wanted their "hometown" to be part of Pakistan. What I found ironic is that despite their piety and wanting to be part of Pakistan, 60 years on, they are shunned in Pakistan. Reminds me of the stranded Pakistani's or Bihari's.
4. Assam. The problem with Assam's Muslim migrants (although that is debatable if they can be called as migrants inside one country at that time) goes way back, even before Independence). Spate himself mentions this and says, "Most of the migrants were Muslim family squatters, and the value of this potential lebensraum is shown by its inclusion in preliminary Pakistan propaganda"
5. Problems with the Chittagong Hill Tracts. Hindu's were 2.0%, Muslims were 2.8%, rest were aboriginals. So while geographically it was uncontested, politically and religiously, it was quite a difficult issue because I still cannot see any difference between tribals (aboriginal) religion and Hindu religion (if there is any such thing!).