Article 1, §9 specifically forbids the Congress from passing any ex post facto laws, and §10. does the same for the states. Since the FTC already gave consent the first time around, this hinges on whether the FTC as an independent agency is considered a proxy for Congress. Note that the attorney generals' separate suit does not have this concern.
Does that prevent Congress from passing laws criminalizing ongoing behavior by corporations, or just from prosecuting acts from before the law was passed?
Not a lawyer answer: the latter. Note, though, that a law criminalizing behavior specific to one person or corporation could be considered a bill of attainder, which is prohibited by the same clauses in the constitution.
You bring up an interesting point, but the Sherman and Clayton laws were passed over a century ago. Perhaps the FTC went against the will of Congress by approving them in the first place, which brings up its own questions around administration of the laws by the executive branch.