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.
(..) ...on the street for a report in Lower Manhattan. Sweetheart, it's all right. It's all right. It's all right. Rough night. It's gonna be all right. Where have you been? Hi. My father died. There was a funeral. (..)2012 The Amazing Spider-Man
(..) ...I don't have much education. You know that, Peter. Hell, I stopped being able to help with your homework when you were . What I'm trying to say is... ...I know it's been rough for you without your dad. And I know we don't talk much about them. - Yeah, it's all right. - No, it is not... (..)2012 The Amazing Spider-Man