A federal judge ordered three college students to cancel a Sunday presentation at a computer hackers’ conference where they planned to show security flaws in the automated fare system used by Boston’s subway. The temporary restraining order, issued by a U.S. district judge in Massachusetts, prevented the Massachusetts Institute of Technology students from demonstrating at the Defcon conference in Las Vegas how to use the vulnerabilities to get free rides. The Electronics Frontier Foundation, which is representing MIT students Zack Anderson, R.J. Ryan and Alessandro Chiesa, plans to fight the order, said Jennifer Granick, the group’s civil liberties director. The Massachusetts Bay Transportation Authority said in a complaint filed Friday that the students offered to show others how to use the hacks before giving the transit system a chance to fix the flaws. MIT is also named in the suit.