Although both of the above methods provide a better score for the better closeness of prediction, still cross-entropy is preferred. Is it in every case or there are some peculiar scenarios where we prefer cross-entropy over MSE?
Cross-entropy is prefered for classification, while mean squared error is one of the best choices for regression. This comes directly from the statement of the problems itself - in classification you work with very particular set of possible output values thus MSE is badly defined (as it does not have this kind of knowledge thus penalizes errors in incompatible way). To better understand the phenomena it is good to follow and understand the relations between
You will notice that both can be seen as a maximum likelihood estimators, simply with different assumptions about the dependent variable.