It sounds like you made excess contributions of $1500 in 2012 and $1800 in 2013, since you are only allowed to contribute up to your earned income. See
this article for more information about how excess contribution rules work. Basically you owe a 6% penalty tax each year on excess contributions. These excess contributions build up from year to year, so if you do nothing you would owe 6% of $1500 ($90) for 2012 and 6% of $3300 ($198) for 2013. The excess contribution keeps accruing the 6% penalty every year until you correct it. You can correct it by withdrawing the excess amount from your IRA (talk to your IRA provider about how to do this), or by contributing less than your maximum in a future year.
The article says that if you filed this year's tax return on time (which you did), you have six months after Tax Day to correct an excess contribution from 2013. So if you withdraw the $3300 (plus any earnings on that money) within six months from now, you will get out of paying the 6% penalty for 2013. If your IRA did go up in value, you will likely have to pay your regular income tax rate plus a 10% early withdrawal penalty on the gains (but not the principal). You will need to file an amended tax return to report this situation.
The deadline to correct your 2012 excess contributions has passed. You will need to file an amended tax return to pay the 6% penalty. You may owe interest on this late payment as well.