He's 'having a rough time (of it)'. = He's 'going through a rough time'. [=he is having a difficult time; his life has been difficult recently]
The project still has a few 'rough edges'. [=the project still has a few things that need to be changed or finished]
Don't 'be so rough on them' [=don't punish or criticize them so harshly] for making a mistake.
(..) That's just what the bird wants us to do! So, Dr. Koothrappali, long flight? hours. Oh, that's rough. Not at all. Did you know that when you fly transcontinental without your wife, you don't pray for the plane to crash? Can you please talk (..)2014 TvShow: The Big Bang Theory Title: The Clean Room Infiltration Season: 8 Episode 11