"He had previously taken out $8000.00 which would be taxable."
Okay, then. It seems the Gross on that 1099-R is correct.
"He then took out the $50,000.00 with no withholding and returned the $50,000.00 one month later all from the same IRA."
Returned? You told us this: "He had actually taken out $50,000.00 from his IRA in October 2020 for personal reasons and made a contribution of $50,000.00 in November."
Did you want to treat this as a Rollover amount, or as a Contribution? If contribution, does this qualify as pre-tax/tax deductible? What sort of IRA is this: Traditional? Roth? Is there Basis in any account? It doesn't have to be the same one IRA account.
"I put it in as a contribution and it came out with him owing $3000.00!"
What makes you consider this to be wrong?
"Level Up" is a gaming function, not a real life function.