But Flick is eager to keep Thiago, labelling the Spain international an "amazing player".
"I don't think about it at all, that Thiago could leave us," the Bayern coach said after Saturday's 4-0 win over Wolfsburg.
"I have always said that Thiago is an amazing player who can give a lot to a team. Therefore, I do not think about that at all.
"And I think after such a game and such a season, you have to accept as a journalist that not every question can be answered."
Thiago arrived at Bayern from Barcelona in 2013, winning the Bundesliga in each of his seven seasons at the club.
Earlier in the week, Flick revealed their had been no progress in contract talks with the Italian-born midfielder, but was full or praise about what his player could add to the team.
"There is no [contract] news. We always talk, almost every day, but there is no news," Flick told a news conference before Bayern's final league match against Wolfsburg.
"I see him every day at practice and at the games. There are always so-called experts who have their own opinions. When you see him on the pitch and in training, you see his extraordinary quality in possession of the ball.
"But he has now also shown that he can play against the ball. For me there are no two opinions about Thiago's quality.
"He gives the team a little something extra. He is an exceptional player who gives a team that certain something. That's my opinion and there is no other one."
Bayern completed their successful Bundesliga season by reaching 100 goals, as Kingsley Coman, Mickael Cuisance, Robert Lewandowski and Thomas Muller scored against Wolfsburg.