In a nutshell, a CT scan takes less time and is less expensive than an MRI scan. An MRI is used for more discreet lesions particularly around the nerves and brain, but for more "bulky" lesions (tumours etc) a CT scan is more appropriate.One would not need either for the diagnosis of herniae.In asnwer to your question...yes a CT scan would have shown other problems despite looking for kidney stones based on my provisos above.
It is a question of professional judgement as to which investigation to use..MRI or CT.