I don't know a lot about banking in the UK, but I used to work for a US bank, and the bank would always attempt I think three times to debit accounts before sending off a "we couldn't debit you" message, so if you put money in to cover the debit, you might be able to catch it. Wait a few days to make sure nothing stray goes out and then call the company debiting you and have them put it through again.
It won't affect your credit unless your bill is more than 60 days overdue.