Wenger admits he expected Fabregas to spend the rest of his career at the Nou Camp after he joined them from Arsenal for £40m in 2011.
Fabregas faces the Gunners for new club Chelsea tomorrow after quitting Spain in the summer.
Wenger said: "It didn't go as well as he imagined it.
"I felt that when he goes back to Barcelona he will finish his career there or come back to Arsenal.
"It was the fact that he left Barcelona much earlier than everybody expected. Why? I don't know. He can explain that much better."
Wenger had first refusal on resigning Fabregas but passed on a £30m deal, allowing Chelsea to snap him up.
"We were in search of more up front and more defensive opportunities than creative midfielders - we have many," said Wenger ignoring the fact Fabregas has been playing in a deeper role under Jose Mourinho, alongside Serbian Nemanja Matic.
Rumours persist that Wenger has never forgiven Fabregas for the hard-nosed methods he employed to engineer his move to Spain.
Yesterday he responded to claims Fabregas was unhappy that his old boss didn't send him a birthday text message and did not respond to the one he sent to Wenger.
"Maybe sometimes you get so many messages that you forget some," said Wenger. "You cannot reply to everybody. It happens. If I did it, I apologise.
"I don't see why he should not be happy with Arsenal or with me. The most important thing is that he is happy.
"I think Fabregas will have a great career because he's a great player. When he looks back at his career he will find that Arsenal and myself had a very positive impact on his career.
"Nobody can dispute that.
"I have no personal animosity against Fabregas. I wish him well. He's a great player and a person and player I love.
"Once he left us, he left us. We are all professionals and we have to accept that."
Wenger also confirmed he had been interested in Chelsea's new striker Diego Costa - who already has eight goals since joining from Atletico Madrid - and Belgium playmaker Eden Hazard, landed from Lille for £32m in June 2012.
Asked why he had miss out on both, Wenger said: "Who is the agent of Costa? Mendes, okay," referring to Mourinho's agent Jorge Mendes.
"With Hazard we were on the case, but didn't get him for financial reasons. He's an amazing player of course.
"At 20 and 21 he was voted for two years consecutively the best player in France by his peers. That didn't happen to many people.
"Costa has done fantastically well, I must say. He has all the aspects of a striker that you like. He's focused, always determined, ready for a fight and I'm impressed."
