If you are not deemed to work ‘within IR35’, no taxes should be deducted and if any taxes are deducted you should take it up with the party paying your fee.
However, the determination of whether IR35 applies is solely up to the public or private sector body (NHS Trust, Health Board or private client) into which you contract. If you disagree with the decision they have arrived at, you can appeal the outcome with the client. Based on the guidance notes to the relevant legislation, it seems as though they will make the deductions of tax and National Insurance contributions and you will have to claim it back from HMRC and make the relevant representations directly to HMRC.