You need to watch how your pension is paid.
Lots of companies pay the pension contributions before tax. This reduces your total taxable income and you are taxed on the rest.
e.g. paid £100,000
5% pension cont = £5000
Total taxable income = £95,000
You then get £12,500 (ish) of that tax free as personal allowance.
You then pay 20% on Anything above £12,500 plus an extra 20% on anything above £50, 250 (ish)
However, some companies pay pension contributions after tax. This means you have paid tax on that money already. To try to neuralise this they often just py 80% of your contorbutions to the pension company, who claim 20% back from HMRC. The end result is that you've only hd 20% tax relief on this money, but should have had 40% - so you need to claim the extra 20% from HMRC yourself.
e.g. paid £100,000
You get £12,500 of that tax free.
You then pay 20% of everything over that and an extra 20% again on everything over £50,250 (ish). At this point your pension contrbitutions have not reduced your taxable income (you are paying too much tax because it has been calculated against £100,000-£12,500 not £95,000-£12,500).
5% pension contributions = £5000 but you only see 80% of that leave ypur pay packet (£4000). The pension company claims £1000 from HMRC to make up the rest. You need to also claim 20% (£1000) back from HMRC to get the full tax deducted.