I watched the race. Cavic was touching the wall underneath the water while Phelps was touching the wall above the water. So, it is possible that Phelps pipped Cavic to the wall due to less resistance from the water. But 100th of a second? How do they measure it? That is ridiculous, even with due respect to Omega time-keeping technology.
In any case, I doubt it is possible for Omega to rig the timing in favor of Phelps. For all we know, the timekeeping could have been kept by the Chinese officials and ractified by various IOC officials there.