What's your accounting date?
Just tell HMRC that your accounting date is 31 August, you've presumably filed the 2011 tax return by the 31 August 2012 and HMRC have their dates wrong and the penalty isn't correct. It's all automated so they spam out these penalties quite often by mistake.
Edit: I also assume you filed 2 tax returns for the period ending 31 August 2011 or you were dormant for part of that period?
A tax return can cover a maximum of 12 months, if you incorporated on 10 August 2010 and your first accounting period was until 31 August 2011 then that's longer than 12 months and 2 tax returns are required.
Unless you incorporated and didn't begin to trade immediately.
Did you prepare the tax return yourself or did you pay someone to do it for you?
It sounds like you should have submitted 2 tax returns. HMRC have got the dates wrong but that just means the penalty should have been issued sooner if you only filed 1 return.
Do you mean £2,848 was your profit in your accounts? It wouldn't be your wages as they would form part of your accounts so I assume you mean you paid yourself a dividend.
Tax profits aren't the same as accounting profits, adjustments are made. You're looking at very roughly £600ish of tax.
Edit: And the tax was due in May.
Well no if it was wages you have a tax free allowance but you'd need to put it through as salary.
Why do you even have a limited company at that level of profit? Why are you not self employed?
I suggest you speak to an accountant and don't continue to make a mess of your company accounts as you clearly don't know what you are doing.
You didn't earn it, the company did, and quite potentially yes the company will owe that amount in tax. Without more detailed information on your accounts I can't know exactly what the company owes.