"If you are getting a refund then there is no penalty for filing late and no explanation is necessary."
This statement is not always true.
If you are getting a refund, there can still be a penalty assessed. It will likely be deducted from your gross refund amount.
You are likely to get a letter from the IRS explaining their recalculation. If you disagree with their calculation, you can dispute it or request a waiver.
