There's a thread on it over in Baseball:
link to the thread
By rule, a runner's basepath is a direct line from wherever he is to the base he's trying to acquire. Once the defense begins to play on a runner, he must remain within 3 feet of that basepath. Should he deviate, the runner is out (the ball is not dead, so other runners may advance).
Presumably, after their little huddle the crew in the Yankees-Sox game determined that Youk was outside the allowable 3 feet. This call can be made retroactively, and runners placed accordingly.
Notice that the rule has nothing to do with a direct line between the bases.