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The problem was because the south had a huge population of slaves, and slaves which had a bunch of slaves wanted the slaves counted. The northerners of course did not want that to happen so they compromised that only 3/5ths of slaves would be counted for the purposes of determining representation.
The above answer would be correct if the question was about the Three-Fifths Compromise. The main issue of representation centered around large states who wanted representation to be proportional to population and the small states who wanted a set number of representatives that was the same for every state. If this issue wasn't resolved, there would be no agreement and the Union would be doomed. The Great Compromise was the deal struck to prevent that. It stated that the lower House of Congress, the House of Representatives, would have proportional representation and the Upper House, the Senate would have two reps for every state.
Representation was the first issue discussed because it was the disputed part of the first plan proposed, the Virginian Plan. The undisputed part detailed the branches of the government.