Federal Tax Determination

I am doing the tax return for my deceased brother in law.  It is showing a tax due both in federal & State.  It is showing a self employment tax but he was never self employed.  He did receive a 1099-Misc by his former employer in additional to his pension which he received every year for additional medical expenses above Medicare.  He was on Medicaid in a nursing home and they had to be paid all his income less $45 for misc. incidentals.  What was I suppose to say this $1000 was for?  He never paid income tax on his past years.