In general, the New Deal raised questions about the jurisprudential distinction between the "public" and "private" spheres of economic activity. The question at the time was whether U.S. Congress was infringing on the property rights of private individuals by regulating sectors of the economy associated with a public good. Furthermore, any act of Congress that gave new regulatory powers to the President were suspected of violating the limited executive powers of the U.S. Constitution.
There were three big challenges to the New Deal on May 27, 1935 in the U.S. Supreme Court: Schechter Poultry Corp. v. United States, Louisville Joint Stock Land Bank v. Radford, and Humphrey's Executor v. United States. Schechter violated Due Process Clause, Louisville violated the Fifth Amendment's Taking Clause, and Humphrey violated the limited powers of the President, particular the FTC Act.
The constitutional challenges to economic regulation around the time of the New Deal is often referred to as the Lochner Era in the literature. In general (although not without exceptions), this era of the Court was characterized by the common practice "to strike down economic regulations adopted by a State based on the Court's own notions of the most appropriate means for the State to implement its considered policies" (source: Stephen Breyer, who knows a bit about the Court).