Difference between "is not" and "cannot"

For rules in logic games, is there ever any relevant difference between rules that state, for example, "If A is in, B is not in" and "If A is in, B cannot be in"? Are we always to take the contrapositive of "B cannot be in" to be the same as "B is not in"? Couldn't you reason that the opposite of "B cannot be in" is "B can be in"? And then saying that "B can be in" wouldn't be definitive enough to make the same inference as "B is in"