Question statement: 

I deposited TiN on SS 201 substrate by reactive magnetron sputttering. 

After the sputtering process patches appeared on the surface of my target - its surface got rough.

What could be a possible reason for these patches?

Answer for reference:

Your target was bombarder by ions of plasma so it means that some amount of matereal was sputtered. 

In some literature the zone of target which changes its surface roughness or chemical composition during sputtering is called erosion zone. 

Here you can read about modeling of Studying Target Erosion in Sputtering Magnetrons

chrome-https://www.plansee.com/fileadmin/user_upload/RM12_Studying_Target_Erosion_in_Sputtering_Magnetrons_Using_a_Discrete_Numerical_Model.pdf