Nationality Checking Service Problems

My husband attended a NCS appointment in Hamilton last week.  Today through the mail he received a letter from the Home Office stating that payment had not been included in his application and to send details within 14 days or his application would be cancelled. 

He definitely included the payment slip because the woman checked it over at the appointment and gave him a receipt.  I'm assuming the payment slip has been lost along the way but now i'm slightly concerned that we are going to be charged twice.

Is the naturalisation fee supposed to be taken at the appointment itself or by the Home Office? 

He sent off the new payment slip with a photocopy of the receipt and an explanation so hopefully it will be alright.