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.
(..) Where we lay, our temples were blown down and, as they say, lamentings heard in the air, strange screams of death. 'Twas a rough night. (SHARP INTAKE OF BREATH) Confusion now hath made his masterpiece. Most sacrilegious murder hath broke open the Lord's anointed temple (..)2015 Macbeth