Mishraji - assume for a moment that the train gets filled to capacity (i.e., all seats and standing places are occupied till the specified limits - not overcrowded, but just upto capacity) at the starting station itself (which is very common in Mumbai locals). What is the solution to this so that people do not have to travel like commodity? Is the solution, then, to not halt the train at the next station? Who is going to check how many people got down, how is this to be done? Apply the same question as to how this is to be determined before selling tickets. Is that feasible at all? Are tickets to be sold by looking at each passenger and counting how many have got in so far?

For charges being deducted while refund - look at it this way: Its a business and its done for profit. There are salaries to pay and there are returns to be shown. Railways is not a non-profit organisation otherwise terms like revenue and turn-over would not apply to it.