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.
(..) I'll even wash your clothes. - Is it a deal? - No, it's not a deal. What do you want me to do? I've got no place to go. You've had a rough day today. Go to sleep, and we'll see tomorrow. You've been really great with me, Leon... and it's not always like that. (..)1994 Léon: The Professional