Didn’t exclude VAT payment to HMRC from my profit

Hello, I am a sole trader selling different products online with no tax experience, two years ago HMRC contacted me to send them all my takings between 2013-2016 as my turnover was over the threshod and I wasn’t registered as VAT business, I was clueless didn’t know what is VAT and how it works, I had to pay £30,000.00 +Penalties I made a loss for a period of two years due to my ignorance. Now I want to get back a partial of this payment as I over paid in my self assessment, the amount £30,000 wasn’t deducted when I sent my tax return (2013-2014)it was sent as profit, is this means HMRC owes me £8700? £30,000 x 20% = £6000 and £30,000 x 9% (Class 4 NIC)= £2700. £6000 +£2700=£8700. Your helps is very appreciated. Thank you