Return of excess 401k contributions after deadline

Hello, thanks for the help.
My wife changed jobs and over-contributed to her 401k.
We discovered this long after it was possible to get the contribution returned by the deadline.
Turbotax flagged the issue during tax-time made some adjustment and I think it included the excess contribution as income, though I'm not certain.

Do I need to re-file and if so how?  I looked it up and there was an answer for doing so before the deadline but couldn't find an answer for after the deadline.

Thanks!