In particular, Necessary and Proper as it relates to the taxing power, which the challenged statute relied upon, having been passed decades before the scope of Commerce Clause powers began their expansion, let alone Wickard v. Filburn.
The party that wants the precedent reversed loses in the lower court (because the lower court is bound by current Supreme Court precedent) and appeals to the Supreme Court. The canonical historical example is Brown v. Board of Education, which was appealed to the Supreme Court explicitly to ask them to reverse Plessy v. Ferguson, which lower courts had relied on as precedent.
Additionally, one can argue that the state of the world has changed enough that assumptions made by the USC at the time of precedence require reversal.