You're mixing up the "physical" steps and the array indexing. In RK methods, the intermediate steps are evaluated between collocation points, but that doesn't mean you need to use fractional indices to the arrays. y(k) stores the kth step of y, which happens to be located at t = t(k) = t0 + k*h; (or maybe (k-1), depending on whether you're storing t0 as t(k=1)).
You can evaluate the rate equations at t = t(k) + h/2, y = y(k) + (h/2)*(some slope). But again, that's not the same thing as t = t(k+1/2), y = y(k+...).
As an aside: do you really need to keep all the intermediate calculations at each step? Typically these are stored as temporary variables that get overwritten at each step. That avoids a lot of indexing issues.
