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.
(..) It appears he had a series of late-night ER visits just over six and a half years ago. Well, must have been a rough time in his life. It was. He was getting divorced. Mm. Taken together, this constellation of injuries (..)2016 TvShow: Bones Title: The Murder of the Meninist Season: 11 Episode 12
(..) Look at that. Donuts. There's over a dozen here. What do you think I am, you? I figured some emotional eating might help. It's been a rough couple weeks for the Flyers. You know what, I'm pretty sure Bones is causing it. You think Dr. Brennan is a jinx? I don't know, (..)2016 TvShow: Bones Title: The Murder of the Meninist Season: 11 Episode 12