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 said you gave Barbossa my name as yours. Why? I don't know. I'm sorry. Blacksmith's hands. I know they're rough. No. I mean yes, they are, but... But don't stop. Elizabeth. It's yours. (..)2003 Pirates of the Caribbean: The Curse of the Black Pearl