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.
(..) Oh, look at you. Heh? He likes me. Oh, oh! I'm sorry. Pollito is usually very friendly. He had a rough night. Well, we really should be going. Girls, come on. That is a pity. Young love is beautiful, no? No! (..)2013 Despicable Me 2