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.
(..) If I ever need help, who's a better consigliere than my father? That's it. - Thank you, Papa. - I'm happy for you, Carlo. Mike... Why am I out? Things may get rough with the move. Tom. I advised Michael. I never thought you were a bad consigliere. I thought Santino was a bad Don, rest in peace. (..)1972 The Godfather
(..) She threw it all away just to make me look ridiculous! And a man in my position can't afford to be made to look ridiculous! You get the hell out of here! If that goombah tries any rough stuff, tell him I'm no bandleader. Yeah, I heard that story. Thank you for dinner and a very pleasant evening. (..)1972 The Godfather