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.
(..) An entire scare floor out of commission. What else can go wrong? Oh... what a day. We're just going through a rough time, sir. Everyone knows you're going to get us through it. Tell that to the board of directors. ( slurping ) (..)2001 Monsters, Inc.