Affected partition quite a bit. Punjab and Bengal were the only provinces that had to be split. While both had a slight Muslim majority, the large numbers of Hindu and Sikh did not belong in Pakistan.

According to the Mountbatten Plan, Sikhs, Hindus and Muslims met in the Legislative Assembles to vote for partition. If a majority voted to partition, the provinces would be split along religious lines.

When drawing the Radcliffe Line (the border between Pakistan and India), it was these two provinces that presented the greatest challenge. There were many disputes such as in the Chittagong Hill Tracts. The area had a 97% Non-Muslim majority (Buddhist) but was granted to Pakistan.

Another was the Gurdaspur district in Punjab, which had a slight Muslim majority but was granted to India. Population exchange had to take place. Some say Lord Mountbatten took this decision because it would provide geographical access to Kashmir allowing its ruler to opt with India. Handing Gurdaspur District to India would also put a slight majority of Sikhs in India instead of Pakistan, allowing less of a refugee exodus.

Firozpur despite having a Muslim population was instead granted to India. In Bengal, Murshidabad with a 70% Muslim population was given to India while Khulna with a 51% Hindu population was granted to East Pakistan.

There were a few other discrepancies and debates, and these two provinces witnessed a lot of the partition violence. In some instances partition was decided simply by drawing lines on a map by people who had not even visited these places. East Pakistan still had a sizable Hindu population after partition while West Punjab was mostly emptied of its Hindus and Sikhs.

Here's an important article: http://www.unc.edu/depts/diplomat/archives_roll/2002_01-03/chester_partition/chester_partition.html

And I found this documentary to be quite helpful as well: https://www.youtube.com/watch?v=amnevwW0MJo