Need help with intake and exhaust manifold

So I was trying to change the gaskets on my 225 /6 and when trying to take the two nuts on the exterior of the exhaust, the two nuts that are on each end of the engine that are supposed to be brass, the studs started to come out with the nuts. I know that the nut must be rusted to pull the stud. But should the stud pull out of the engine and should water leak from there? Any help must appreciated. Trying to get the car on the road before school on monday.