I had a similar problem. Took almost a year to correct it.
The IRS is very good about correcting their errors.
The first step is to go to IRS.gov and set up an account.
It is a pain in the ass to set up, but once you do, you can do damn near everything from this account, including past return data and current status and fines/penalties owed.
This is your first step
Thanks for that tip about setting up an account.