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.
(..) - How many are there? - Call every lab you know. Tell them to put the spectrometers on the roof and calibrate them for gamma rays. I'll rough out a tracking algorithm, basic cluster recognition. At least we could rule out a few places. Do you have somewhere for me to work? Agent Romanoff, (..)2012 The Avengers