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.
(..) Mind if I join the fun? - Certainly. How you feeling? Like a Chihuahua that's being tumble-dried. Well, it's been a rough week. If it makes you feel any better, I coughed up everything but my kidneys on my first ride. Shit. Sorry. (..)2013 Gravity