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.
(..) Oh, come on. It could be worse. Yeah, Joy. We could be lying on a dirty floor. In a bag. Okay, I admit it. We had a rough start. - But think of all the good things that... - No, Joy. There is absolutely no reason for Riley to be happy right now. Let us handle this. (..)2015 Inside Out