You are able to change your site settings to display prices on the site with or without tax (VAT) added. Typically B2C shows prices with VAT added, whereas B2B tends to add VAT at the checkout stage.
The system calculates tax on a line by line basis in accordance with the UK HMRC VAT Guide section 17.5.
It is therefore possible that on an invoice with multiple lines, if you manually check the VAT on the total NET amount at the bottom of the invoice, it may be a penny or two different to the line-by-line calculation because of rounding.
This is expected and is in compliance with the regulations.