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.
(..) That's too bad,Jeff. I can't be lucky every day. Forget I called. Yeah, I sure feel sorry for you. Gunnison. must be rough on you thinking of me wearing this cast another whole week. That one week is gonna cost me my best photographer, and you a big assignment. (..)1954 Rear Window