Maybe I'm dumb but why are HMRC actually paying you back as it should be the employer who owes the difference for non payment??
Unless you actually mean that she was charged tax on the 22p?
Ultimately, you pay tax for most mileage, as its seen as a benefit, and therefore does she also get given an essential car users allowance as this will also add to the tax liability. Dependent on how the company pay the allowance, it could be that the tax is paid at source. Double check which way, as she may have an outstanding tax liability if its not taken at the point of wage being paid.