What issues divided the various ethnic and religious groups of the middle colonies?
The "middle colonies" traditionally include New York, New Jersey, Delaware and Pennsylvania. These were attractive regions with rich soil, diverse ecosystems, established cities with deep-water ports, and unique political liberties.
The various religious groups were largely Protestant factions: there was no significant presence of any religious denomination other than Christianity, perhaps with the exception of some scattered Jewish communities. While much has been made of the importance of religious freedom in the time and period, it was largely freedom of Christian religion that was actually addressed. Consider that profession of Christianity was grounds for citizenship; a remarkably open-minded policy by the standards of the time, but hopelessly discriminatory by today's standards.
Some of the denominations included Anglicans, Quakers, Methodists, the Dutch Reformed Church, and Presbyterians. Each tended to be favored by a particular social and ethnic group in a particular region - for example Anglicanism was more prominent among the wealthy and Loyalists in the South, and the Presbyterians were largely Scottish or Irish.
Ethnic groups were, again, not terribly diverse by modern standards, being almost entirely from Europe. The predominant nationalities were English, Scottish, Irish and German, with some Nordic communities. Socioeconomically, there was a greater proportion of middle-class farmers than aristocrats or poor (the trip to America no being free, after all) although there was a large population of indentured servants. There were, of course, slaves, comprising around 10% of the total population.
The majority of the issues dividing these groups were economic ones, such as rules of land ownership, and political ones, such as how to deal with the Native Americans obstructing further settlement. Many of these conflicts directly challenged group identities; for example, the Quakers were pacifists, and would not uphold political action that would lead to violence. Likewise, the various groups sought to maintain internal cohesion and identity, and rarely intermingled; thus a conflict was often one which pitted an entire community against another. The Great Awakening, often called America's first religious crisis, saw a shakeup of some of these identities, with some communities such as the Quakers never recovering their previous influence.
There were also some problems which arose directly from the homogeneity of these groups and the region; for example, Delaware was difficult for William Penn to govern because it was geographically, politically and economically a mirror image of the Chesapeake Bay area.