是的，确实与一般语法书的讲解有所不同。但你这一句有它的特殊性，即本句虽然有所谓的by-短语，但句中的 surprised 并非过去分词，而是形容词，也就是说这里的 was surprised 并非被动语态，而是系表结构，这里的 by 表示原因。事实上，这里不用介词 by，也可以用介词 at。即：

She was very surprised by what he had said.

=She was very surprised at what he had said.

英语中某些表示精神状态、感情、反应意义的形容词（形式上由过去分词转化来）具有类似用法。如：

I was very delighted at / by your news. 你带来的消息让我很高兴。

Everyone was very shocked at / by her behavior. 她的行为让关家都为之愕然。