One thing being overlooked is why there were arsenals in the individual states in the first place.

One of the reasons why there were arsenals, as I understand it, is that one of the requirements for admission to the Union was that the states had to have and maintain their own Militia. These Militia were in fact the "ready reserves" for the National Army so as the United States would not have to maintain a powerful standing army for several reasons including the use of that army against the states.

So Therefore those states felt that they had a right of ownership of those arsenals.