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.
(..) Hearts and flowers? That's not something I know Ana please - its you that is changing me. Let me touch you. Let me. - Are they burns? - I had a rough start in life. - That's all you need to know. - Okay. The woman who gave birth to me, was a crack addict. And a prostitute. (..)2015 Fifty Shades of Grey