The site is reporting that Paramount decided not to pick up the option on the actress, news that was confirmed by Variety, but Deadline reports that the decision was ultimately up to director Michael Bay. It was said that Bay is finishing up work on the script with writer Ehren Kruger and they are, "giving Shia a new love interest makes more sense for the story," according to one of the site's sources.
While there has been friction in the past between Fox and Bay, including an interview where Fox compared Bay to Hitler, the Variety story indicates the decision was unrelated to those remarks.
We'll be sure to keep you posted with any and all news regarding Transformers 3 as soon as we have more information.
Transformers: Dark of the Moon was released June 29th, 2011 and stars Shia LaBeouf, Rosie Huntington-Whiteley, Julie White, Kevin Dunn, Josh Duhamel, Tyrese Gibson, Alan Tudyk, John Malkovich. The film is directed by Michael Bay.