It can happen that money gets paid into your business bank account that is not from sales. It can also happen that adjustments are made to sales that are not the result of invoices raised or credit notes issued.
This will be fine until HMRC look more closely at your records and this can be prompted by the discrepancy between your sales as shown in your accounts and the total outputs declared on your VAT returns for the same period.
When they come knocking you need to have a satisfactory explanation. Otherwise HMRC may contend that these discrepancies represent unrecorded sales and seek an adjustment to your taxable profits, with more tax and probably penalties and interest.
A little more care at the time can save you much grief later.
In a similar vein, HMRC will also obtain information from your card provider and making assumptions about the relationship between card and cash takings, compare the results with the sales declared either in your accounts or VAT returns.