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.
(..) I'm not crazy, John. I'm not saying that you're crazy, okay. And I'm not talking about a shrink. So we turned to the Church, Father. It's what my parents did when they hit a rough patch... and it worked for them. I understand, of course. But you two hit more than just a rough patch. (..)2014 Annabelle