New York follows the convenience of the employer rule, meaning an employee working remotely can be taxed by NY if they are not working in Indiana due to some business necessity, such as to be near clients.
You can claim a credit on your Indiana return for tax paid to NY. If you did not claim a credit, you can amend your Indiana return.
See I need to amend my state return
If your employer withheld NY tax and you never set foot in a NY office, you can instead file for a refund of all tax. You will likely get audited, in which case you can cite several court cases in your defence.
Read the discussion by @kristinelbly in I work for a NY company, remotely from NC. I spent 1 day in 2017 on site, but my W-2 has full salary...
