Can we say: People have dfficulties understanding grammar. ?
Yes, if you think that there is more than one factor that makes it hard for them.
For example, confusion with tenses, no articles in their native language, trying too hard to make English conform to their native language's grammar, problems with pronouns... those could all be considered "difficulties."
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.