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Its correct that you have been taxed but should only have suffered the 20% basic rate tax on this pay in lieu position,however if this has been made in isolation from the main salary run, then the seemingly additional tax may well be due to the fact no personal tax free allowances have been allocated, so on £5000 you would have suffered £1000 tax and only have received £4000
Could this be the case?
If not - and you have been alocated personal allowances, and your payslp does show a 40% tax suffered, then you have two choices
1) Go back to the employer and insist they rerun this final pay with your highest rate of tax (which is 20% nasic rate) or
2) If you are not planning to work again then you can ask HMRC to review the position for you after 05/04/2015 - by sending in a letter and the P45 (keep copies for your own records)
As for the 0.5 half holiday day, this is entirely a matter between you and the employer - but if you feel this is incorrect then ACAS are a body who can liase with your employer for you -
see link here http://www.acas.org.uk/contact
Let me know if I can be of any further assistance with this matter.