Question

Why did Southern and Northern delegates disagree over whether the new Congress should have the commerce power

Answer 1

The Southern side particularly was against it (and the Northern was in favour), as the South feared that it could lead to the end of poverty, which would be economically bad for the South.

Answer 2

I believe the answer is: Southerners feared it would lead to the end of slavery.

By giving the congress with the power to control the commerce, the congress could create a regulation regarding the type of labours that the southerners can use. When this happen, the Southerners believe that the Congress would leverage the power to eliminate slavery which they relied on for their plantation and could destroy their economy.