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.
(..) ...you let us know. So who did the two guys from Providence? Jimmy Pappas. What happened to Jimmy Pappas? Jimmy had a rough month. Jimmy had a heart attack in jail... ...and then he got himself knifed at Boston City Hospital. I believe it's been in the papers. You seem quite happy with that result. (..)2006 The Departed