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.
(..) - The two enhanced? Wanda and Pietro Maximoff. Twins. Orphaned at ten when a shell collapsed their apartment building. Sokovia's had a rough history. It's nowhere special but it's on the way to everywhere special. - Their abilities? - He's got increased metabolism and improved thermal homeostasis. (..)2015 Avengers: Age of Ultron