I am trying to do taxes for my Father. He has a 1099-R(Pension), 1099-SSA and then a 1099-R(IRA payout and conversion to Roth IRA). Why is this counting as Self-Employed?

None of those forms are considered self-employment income. Check your entries to make sure everything is entered in the right place. Was something entered as a 1099-NEC? That's the self-employment form.

The 1099-Rs should be under IRA, 401(k), Pension Plan Withdrawals (1099-R) and the SSA-1099 is under Social Security (SSA-1099, RRB-1099).