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.
(..) He'll know who I am. All clear. No pathogens. Dr. Cassandra Railly of the CDC. Where's your identification? I lost it. I hit a few rough patches on my way up from Baltimore. Baltimore? On foot? Tell me, Ms. Railly, how did you avoid the West Seven Quarantine Zone? (..)2016 TvShow: 12 Monkeys Title: Lullaby Season: 2 Episode 8