This is outlined in Trinity and Morpheus' earlier conversation with The Oracle. Her "choice" is to have faith in Neo, to lead him into a sexual relationship with Trinity (creating the profound attachment that leads him into making the decision to take the left door) and into an open conflict with Smith rather than simply fulfilling her normal role of guiding him back to the Source to reboot the Matrix.
This is an astoundingly risky move on her part (one that could very easily lead to the death of the human race and the destruction of The Matrix) but she seems quite sanguine about her decision by this stage:
Trinity: What happened?
Oracle: I made a choice and that choice cost me more than I wanted it to.
Morpheus: What choice?
Oracle: To help you, to guide Neo. Now, since the real test for any choice is how we make the same choice again, knowing full well what it might cost, I guess I feel pretty good about that choice, `cause here I am, at it again.