One tricky piece in distinguishing substantive merits from jurisdiction is the problem of the "jurisdictional element"--an element that Congress must include to show it possessed legislative power ("legislative jurisdiction") to enact the statute and regulate the targeted conduct. The most common jurisdictional element is that the conduct "affected interstate commerce" for Commerce Clause legislation (recall US v. Lopez).
The term "jurisdictional element" creates confusion--doesn't that mean the failure of that element deprives the court of jurisdiction. The answer is no, because we distinguish Congress' "legislative jurisdiction" from the court's "adjudicative jurisdiction." The failure of the former represents a failure on the merits--the failure to satisfy some element of the charge; it so happens the element is constitutionally required, but it remains an element. The court has original adjudicative jurisdiction under 18 U.S.C. § 3231 "of all offenses against the laws of the United States."
The Eighth Circuit held that the federal government failed to prove the commerce element in a sex trafficking prosecution (the use of money and a car that had been manufactured in another state was not enough). There is no discussion or suggestion the district court lacked jurisdiction. The district court properly acquitted because the charge failed.
