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 almost told me your name! You're gonna get stuck in a situation you created! So if you wanna throw bad looks around, throw 'em at a mirror! You kids shouldn't play so rough. Somebody's gonna start cryin'. Mr. Blonde. Shit. You're fuckin' kickin' me. What happened to you? Figured you were dead. (..)1992 Reservoir Dogs