Terms and Conditions on their site:
6.15 Your bill will normally include your fixed Charges for the next period and any administration fees along with Charges for your use of the Three Services in the UK in the last period and outside the UK in prior periods. It may also include an amount to repay the cost of your Three-compatible Device (depending on the payment scheme you have chosen). Your initial bill may also contain a Connection Charge. VAT will be added to your bill where appropriate.
Not sure what to suggest. For end users, prices normally include VAT. For business packages, they exclude it. So I agree, this does seem a bit off. Not sure if you can do anything about it.