If you have an invoice with multiple lines on it and you then check the VAT amount is the correct percentage of the NET amount then you may find it to be a few pennies different from what you'd expect.  This is because VAT is calculated on each line and rounded to two decimal places.  Then at the bottom of the invoice the sum of these calculations is used as the total VAT due.  When you have multiple lines on an invoice the sum of these rounded figures can sometimes be different to if you add up the total of the NET figures for each line and calculate the relevant percentage of that.  This is expected and correct as per Section 17.5 of the HMRC VAT Guide.