It is because there is excess demand at the price charged by the MTR or buses companies. Therefore, consumers are served by the first come first served basis on the seats. You can imagine if the MTR or buses' companies charged higher prices that are closer to the market clearing prices, the number of people standing will be lesser. As the companies do not charge higher prices, passengers from the bus terminus can have seats, but for those passengers from the bus stops along the route, they might stand in the buses.