It was a hoax. You need multiple doses of the vaccine over a span of months for it to work. They didn't do that.

http://www.scientificamerican.com/article.cfm?id=how-cia-fak...

The misguided vaccine program in Pakistan was started in a poor neighborhood of Abbottabad, no doubt to give it an air of legitimacy. Yet after the first in a standard series of three hepatitis B shots was given, the effort was abandoned so that the team could move to bin Laden's wealthier community.