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.
(..) - But the radish are almost good. - Fine. Hi. Let's go. Just so you know, he's had a rough night. Just like you, apparently. The day starts at a.m. sharp with the nurse. He needs to hours of care every morning. (..)2011 Intouchables