But you knew you had self employment - for 2014/2105 as this is what this whole issue is about - so by the tiem they made the refund you should have alerted them to the situation straight away and HMRC dont know you earned under the personal allowance until you submit your tax return at which time they will see the tax repayment is correct with it having been paid to you.
We have already established that £100 penalty is for late registration and the other £200 you advise relates to late payments on account - which I have answered fully - how this would have arisen.
The refund has nothing to do with the penalties, but you keep drip feeding information and I then you ask more and more questions which is far more than this question originally suggested.
1) Get that tax return in
2) establish with HMRC how payments on account arose as you state that 2014/2105 was the first year ever that self assessment tax returns were due - because of this small amount of self employment
3) if they have made a mistake then £200 of the penalties will be reduced to NIL but £100 will still stand for late registration
But you cannot keep expanding on this question, these should either be included in the original question or listed as new questions - as this has been ongoing since 29th Oct and with more and more information revealed each time I have fully answered the previous posts.