Payment Issue - amount mismatch
I've been in touch with Virgin many times over the last month trying to fix a contract expiry / discount mismatch. Last month I spoke to a member of customer retention (3rd attempt of getting fixed after unfulfilled agreements) who offered to have the discount issue fixed and told me she had applied a credit to my account to bring the bill down to it's usual level while it got fixed. Bill came out at the usual level as expected, didn't think anything of it.
Today I've received an email stating I owe the higher amount plus the "amount underpaid" from last month and a late fee.
I pay by direct debit so Virgin should have taken the full amount they wanted if the agreed credit wasn't applied and then I could argued out the rest. I've raised a complaint in relation to the contract/discount issue but I'm now panicking that this underpayment will mess up my perfect payment history on my credit score.
Has anyone experienced similar that can reassure or offer some advice?
[MOD EDIT: Subject title changed for clarity]