Reading this article I’m quite puzzled as regards the use of had been. For me, the sentence as is makes no sense; it’s kind of no finished idea, as though you expected something to follow, which is why I’d use was instead:
The Saudi ambassador to Indonesia, Mustafa Ibrahim al-Mubarak, said he had been "surprised" to be summoned, but would "check what went wrong".
Please compare the following sentence which comes next in the article:
The Saudi interior ministry said the execution had been delayed for more than 15 years until the youngest of the victim's children was old enough to decide whether or not the family would want to pardon Ms Zainab or demand her execution.
Here the use of had been is perfectly understandable, the action described takes place before another action finished in the past.