Williams's troubles with the Blues had no impact on his international career, as he was included in the New Zealand squad for the two-Test series against France in June 2007. He started both Tests, but suffered a serious injury in the second Test, on 9 June, when he fractured his jaw while tackling French number eight Sébastien Chabal. As a result, he missed the whole of the 2007 Tri Nations Series. But despite having his jaw wired and being forced to subsist on soup for several weeks, he made a return to rugby for his club side, Ponsonby, at the end of July, scoring two tries, and started for Auckland in their Air New Zealand Cup match against Bay of Plenty on 3 August, scoring a try in the fourth minute of the game. Coincidentally, this was the first time that Williams and his younger brother, Jay, had played together as locks in first-class rugby.
In 2007, Williams was one of the 22 players withdrawn from the first half of the Super 14 season to attend a "conditioning camp", as part of the All Blacks' World Cup preparations. Although he became available for the Blues in week 8 of the tournament, he was left out of the squad that week, was on the bench in week 9, and did not make his first start of the season until week 10, when the Blues played the Cheetahs. A week later he was back on the bench for the Blues game against the Sharks . A few weeks later, "for disciplinary reasons", Williams was left out of the squad to face the Sharks in Durban in a S14 semi-final match—which the Blues lost—and returned home to Auckland. Blues chief executive Andy Dalton told the press that management and senior players had made a joint decision to eject Williams from the team camp over incidents which occurred during the team's stay in Perth, Australia, where they had played the Western Force. "On several occasions (Williams's) behaviour has been deemed inappropriate within team conduct and protocol and on at least four occasions Williams has been addressed by either coach David Nucifora and manager Ant Strachan or the leadership group on behalf of the team", Dalton said. In response, Williams said that he took "a bit of responsibility" for his actions but that "it takes two to tango".
In August 2007, Ali Williams announced that he had signed a new contract with the NZRU that would keep him in New Zealand until the end of 2009 and that he was signing for the Tasman Makos for 2008, so as to be eligible for selection for the Crusaders in the 2008 Super 14 season. Salary cap restrictions prevented a move to Canterbury, but his contract with Tasman has an option that would allow him to be loaned to Canterbury for the 2008 ANZ Cup. Williams was duly included in the Crusaders squad when New Zealand's 2008 Super 14 teams were announced, in October 2007.