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Sorry I am not quite clear, how would my tax free allowence would have been corrected automatically when I submitted my tax return for my private work? All I put in is my tax code (which I think is less than should be) and information from my PD11 again incorrect.
Well one hopes that your employers would have been in contact with HMRC when the changes were made. In any event HMRC should have picked this up from the P11D additional return. Now if this form was incorrectly completed then you must take it up with your employer as well as HMRC. The automatic adjustment would have been between HMRC and the Council and not impinge on your private mileage.
As far as your private work is concerned claiming the HMRC 45p/25p rate is just a normal entry on your self assessment tax return. Care would have to be taken in the event of Council and private work mileages aggregating to over the 10K miles limit.