My mistake. Since you capitalized it I had assumed you were talking about Vattel’s book and not James Wilson’s lectures. But even Justice Wilson agreed that there were limits on a state’s sovereignty.
Yes, and that limit on state sovereignty included not only the civil States, but also the general government of the United States as defined in Article 1, Section 8, Clause 17.
§ 1218. The inhabitants enjoy all their civil, religious, and political rights. They live substantially under the same laws, as at the time of the cession, such changes only having been made, as have been devised, and sought by themselves. They are not indeed citizens of any state, entitled to the privileges of such; but they are citizens of the United States. They have no immediate representatives in congress.
Salmon P. Chase disagreed, asserting in 1854 'we have rights which the federal government must not invade - rights superior to its power, on which our sovereignty depends; and we do mean to assert these rights against all tyrannical assumptions of authority.'