Boateng spent a stint on loan at Dortmund in the 2008-09 season and impressed, before continuing his career at Portsmouth and Milan.
The Ghana international caused a stir when he signed for Dortmund's arch-rivals Schalke last week, and Klopp made comments in jest about the 26-year-old.
Klopp said: "I'm really surprised. I sent him a text message saying 'Why Schalke' with eight question marks, but I didn't hear back from him.
"He was a good lad, up until this morning."
Boateng played a key role in Schalke's 2-0 Bundesliga win over Bayer Leverkusen on Saturday, as a result that snapped a three-game winless run in the German top flight.
And Schalke's new star man has said that he was unhappy with Klopp's comments.
"Many people thought it was funny, but I didn't," he told Sport-Bild.
"Even if 'Kloppo' and I have a good relationship, he's not going to hear me say a bad word about him, but this press conference surprised me."
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