HMRC are within their rights to penalise you for an incorrect return, but with your full cooperation they are unlikely to.
Without knowing your full situation I cannot guarantee any advice I give, so please dont rely on it, but if I were in your position I would do the following:
Based on a return for the 2010/11 tax year you have 12 months to submit an amended return, so that is what you now have to do.
As has been said already, phone HMRC's SA helpline. Say that it was an honest mistake, that you are pregnant, and that its been a very busy/difficult time for you lately etc, and that is why you made a mistake.
It may be the case that you will have to pay some extra student loan back, and this is why the error was flagged up on their system (they share records with the student loan company). If you cant work this amount out yourself, you will need to speak to HMRC about it and let them know - they can help.
Let HMRC know that you fully intend to pay any tax/student loan due and that you did not intent to defraud the system, and they should be fine.
Generally in cases where there is full compliance, and it is a genuine error, they are unlikely to penalise you. If for some reason they do issue a penalty, it can be a % of any tax due, so say 5% for a minor misdemeanour or 100% for a very serious one.
Whatever happens - dont worry about it, and if you arent happy with their determination the appeal system is very good, and worth doing, as many appeals are won.