Is there a way for paying the fees, if there is a payment failure, without the application being rejected?

Important HO contacts:

• Charging Dept (Home office) 01142072918 
• Customer Service (Home Office) 01142072966 
• Email: charging.workpermits@UKBA.gsi.gov.uk
• Fax: 02081963248. 

Explain your observation and authorise them to resubmit the payment.

Lessons:

• Before you send the documents to Home Office, ensure that you have advised the bank of such transactions. The banks have a separate department for fraud protection, unless notified they may block the transaction.
• It is also advisable to track the transaction, to ensure that things are on track.