Someone told me it's similar to the NBA. When the clock goes under 1 it shows zero but it's not actually at zero. So it could be nine tenths of a second but the clock will show zero. Apparently there is some visual thing a light or whatever that comes on telling the ref when the clock is at zero. So on calls like that the claim is while we saw zero, the light hadn't come on yet.
I saw it at least 3 times too and it bugged me, but then a friend made a very good point. The rule is there to stop teams from stalling by letting time run off a moving game clock. The only actual advantage you gain is if you can run extra seconds off and we're talking split seconds not 3 or 4. My only argument against that is the longer the QB can hold the snap the tougher it is on the defense, especially when a QB is trying to draw the defense offsides.
I do wish the NFL would address it though because I see it all the time and I've heard announcers point it out too, that snap was late but no whistle.