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.
(..) Kids, strap yourselves down like I told you. Here we go, honey. Ready, Violet? Ready? Now! This is gonna be rough. Robot's in the financial district. Which exit? - Traction Avenue. - That'll take me downtown. - I take Seventh, don't I? (..)2004 The Incredibles