Hi. Another expert here. My name is ***** ***** I have a different answer for you.
No, you don't have to pay $3000 but here's what you have to do. You will have to amend your 2013 return using form 1040x and use Schedule D to claim $11,996 proceeds and $11,600 basis. That way only the difference of $396 will be taxable. You will owe little tax plus some interest and penalties but not much, I am estimating around $75.
Here's what happened. The brokerage firm reported the transaction to IRS, but only the proceeds of $11,996. Since you didn't report it on your tax return, IRS had no way of knowing how much did you purchased it for years ago and therefore assumed the entire $11,996 taxable.
On your notice your received there's a section asking you to respond. Check the box that you don't agree with the adjustment and write "see 1040x" next to it. On the top of your 1040X write the letter type, I am assuming is CP2000 (top right corner, start with CP and #), attach the check with the balance calculated on your 1040x and mail it to the address provided on the notice. Most importantly, DO NOT sign the notice since you don't agree with the changes, but don't forget to sign 1040x.
Let me know if you have any questions.