IRS saying I owe them money from previous debt after filing an amended return. and I already paid that debt, HELP!

I owed the IRS money from 2009 and 2010($2,500). I set up a payment plan in 2014. When I filed my 2014 return they kept all of it, and when I filed for 2015 they kept the rest of my debt and I received the remaining amount on my return. Recently I discovered the tax preparer had filed me and my wife's 2014 and 2015 tax returns as single. I went to a CPA to get that corrected knowing that we may owe taxes. When the CPA file the amended return he showed us that the IRS owed us money. Last week I received 2 letters from IRS, one was a statement saying I owe them nothing form my payment plan, the other one it was from my amended return saying we owe them $3,000 "from a previous debt "we" had". How can this be????? I already paid my debt, they took what I owed from my 2015 return, how can this be??? I don't care If I don't receive any money, but owing them from a "debt" that even they sent a letter saying I owe $0.. Im confused.....???????