In my upstairs bathroom, the toilet was clogged and my brother flushed the toilet unknowingly and it over-flowed causing the ceiling directly beneath it to drip. It happened once before and when the water upstairs was mopped and there was no more water going down it stopped. Same thing happened today, what should I do, I think the water went down from the side of the toilet I'm not sure...

The water did not come from inside the toilet. If it did, you would have a constant leak every time you flushed. The water ran onto the floor and then under the toilet where it found the hole for the drain pipe and followed it through the floor and onto the ceiling. You could caulk around the base of your toilet to lessen the amount of water that goes down that way; but the water has to go somewhere.