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.
(..) She may have a difficult time. Well, can't we take her along? Do you want her to take that chance? Do you want her to be jounced over rough roads... ...and have her baby ahead of time, in a buggy? It isn't my baby! You take care of her! Scarlett! We haven't enough doctors... ...much less nurses (..)1939 Gone with the Wind