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.
(..) l can mend bones in a heartbeat, but growing them back. . . . You will be able to, won't you? l'll be able to, certainly. But it'll be painful. You're in for a rough night, Potter. Regrowing bones is a nasty business. What do you expect? Pumpkin juice? Hello. Dobby? (..)2002 Harry Potter and the Chamber of Secrets