There are some color/size combination variants of given product which are not available for selling. Hence I've unpublished them. But these combination are still available on the pull-down menu of the given product. Is this a normal behavior ?
Yes, that's the normal behaviour. The choices cannot be removed from the dropdowns as they are needed for other combinations. However, the add to cart button is removed if the user selects such variant so that he can't buy it.