Ghee freezes from bottom but water freezes from top, why?

I presume you mean ghee as in the butter. Seen as ice is one of the many solids to have a lower density than its liquid form, it freezes from the top. Ghee is made from hydrocarbons not dissimilar to petroleum, it shares the same properties as most elements of its solid state (at 1 atmosphere) being at a higher density than its liquid state.