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.
(..) Business is good. ["SPIDER-MAN" THEME SONG PLAYING] PETER : New York. Queens. - It's a rough borough, but, hey, it's home. HAPPY: Who you talking to? PETER : No one. Just making a little video of the trip. HAPPY: You know you can't show it to anyone. (..)2017 Spider-Man: Homecoming