Well, to my experience, when i was booking for my boss, the payment went through and his credit card charged.
After waiting for a day or 2, still no confirmation slip. Coz Agoda usually have to CALL the respective hotel to confirm the booking.
Anyway, that particular room that was paid for was fully booked and since the charges was already billed to the card, they honour by giving a room upgrade with no extra charge.
Also once, i accidentally booked an extra night, i called up agoda and they said they will call the hotel to see if can cancel that extra night with no extra charge. A few hrs later, got the email from them and the extra night was cancelled with no charges incurred.

Usually for this case, better to call them right after booking.
Best customer service ever!