In the main events of history of pakistan , after 1947 separation of east pakistan is considered one of the major incident. Indeed this event widely repulsed the two nation theory. But this event took 24 to come to a critical end. Read this
But primary causes which have been catagorised by different authors include;

1. Lack of vibrant political leadership
2. Lack of effective centeral government.
3. Language issue
4. Political differences
5. Civil-military bureaucracy
6. Divison of resources
7. Indian role to boost differences
8. Distance between both part of country.

Infact separation of east pakistan has a long narrative but i have catagorised few points to give bullets to css aspirants.