It appears that you might have lost connection to the Live Chess towards the end of the game or lag might have made the clock times appear distorted.
In any case please know that the Live Chess is one of our top concerns here at Chess.com and we are working very hard to further improve the stability and connection to the Live Chess so that problems such as this do not occur in the future.
So I played a game recently.
My opponent ran out of time,
00:02 - 00:01 - 00:00 - (but no "veclock won")
I didn't win, no message came up. It just stopped at 00:00.
Then I checked my Live Chess profile, which said I lost that game.
UM? I did not, my opponent ran out of time.
Now I got lower rating thanks to that bug...