A Major League Baseball source told the Miami Herald that there was a question whether Bush could or should be the controlling partner in the group when so little of his own money was invested.
Bush reportedly was investing less than $20 million of his own money with the purchase price being $1.3 billion.
Although that issue became a concern for Major League Baseball, it is unclear whether MLB would have blocked the deal based on that.
With Bush no longer in the picture, Jeter would become the controlling member of the group, making him responsible for financial decisions if his group is able to purchase the team, according to the Herald.
There was no indication that there had been a power struggle between Bush and Jeter.
CNN reported that a group led by Tagg Romney, son of former Republican presidential nominee Mitt Romney, remains in the running for the bid to purchase the Marlins.
The Marlins are owned by Jeffrey Loria, who bought the team in 2002 for about $158 million.