1 She had been crying.
2 She was crying.
To understand the difference between the two sentences, we need some specific time, or event in the past which we are thinking about, or talking about. For example, that time might be when we met at the cafe yesterday. We here means me and her.
- I met Suzanne at the cafe yesterday.
- When I met her, her eyes were red. She had been crying.
- When I met her, her eyes full of tears. She was crying.
So in the examples above, we are thinking about when I met Suzanne. Sentence (4) says that she had red eyes because she cried BEFORE we met. They were red because of what happened before.
Sentence (5) says that she was crying AT THE SAME TIME as when I saw her. The crying was not finished. It was still continuing. That's why she had tears in her eyes.
Hope this helps!