When a coin is inserted, how far apart are the pulses? If the time between pulses is relatively constant, you could expect the next pulse to be some many milliseconds (or microseconds) later, for a multi-pulse coin. If no pulse arrives within that window, you know that all the pulses for that coin have arrived.
Once you know that all the pulses have arrived, you know the value for the coin. You also know not to do anything about/with the value of a coin during the window that pulses could arrive.