agoda com - full advance payment taken without intiimation

this is regarding two bookings "*********" and "*********" with mayfair goa on same dates on **th and *st october.
Both bookings are valid as i am going with two family . Both booking condition says " You will pay INR **,***.** to the property on your check-in date of Saturday, October **, ****."
But on *th fen **** the hotel has deducted full amout for both booking well in advance. they said that agoda is routing their booking through booking.com so they deducted entire amount.
Problem is agoda is saying in their website booking nothing needs to be paid till check out date and still hotel is deducting entire money well in advance.
I feel cheated and i need a reasonable explanations why agoda is claiming that amouunt needs to be paid at time of checkout but hotel is doing fully charged transaction (not authorize) in advance