As a remote worker, your income is earned where the work is performed so this would be TN source income.
Since you are a resident of TN and TN has no state income tax related to wages, you should file for a full refund of your IN state income taxes.
You need to file a nonresident IN state income
tax return but report zero "0" IN source income (even though your company is saying the you have IN source wages).
You may need mail in this nonresident IN
state income tax return and include his state W-2 information. You will want to
include an explanatory statement with your IN return stating your situation
(that your IN employer withheld IN taxes from your wages in error because you are a remote employee of the company and your a permanent resident of TN)