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.
(..) when I'm speaking to you? It's very rude not to look at somebody in the eye when they're talking to you. It's okay. Don't worry. You're having a rough day. We shot the wrong man. I can fix this. I have a new plan. We need to find a new double. One that is simple enough to be manipulated completely. (..)2012 The Dictator