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.
(..) And you're just ignoring her. - A giant brain? Yeah, there's a giant brain, there's a shifty character... I'm going to follow this guy. I'm going to run his plates and if it gets rough, so be it. I miss you, Happy. - Yeah, I miss you too but the way it used to be. I don't know what's going on (..)2013 Iron Man 3