My invoice says payment £0.00 at the end when the balance due is not £0 why has this happened?

I can share some information with applying customer payments to invoices, @contact-ajproduc. 

You may have turned on the credit memo auto-apply feature. This will automatically apply credit memos to customers' balances or open invoices. You can turn off this feature and then delete the payment that was automatically linked to the invoice. 

Here's how to turn off the credit memo auto-apply feature:

1. Go to Gear icon (⚙) and choose the Account and settings.
2. Click the Advanced tab and select Edit (✎) in the Automation section.
3. Toggle to turn off the Automatically apply credits option.
4. Select Save, then Done.

Then, you can open the invoice and click the payment link below the PAID section of the invoice page. Click More at the bottom and select Delete. 

Here's more information on how to record invoice payments in QuickBooks Online (QBO): Record invoice payments in QuickBooks Online. 

Let me know if you still have questions in applying customer payments and or anything else by leaving a Reply below. Take care and have a great rest of the day!