That the Giants came back and won three games with a 12.5% chance doesn't make the percentages wrong. What it means is that only 12 times out of 100 will it happen. That just happened to be one of the 12.
In this case, yes, four times out of 100 the Nationals would come back. But 96 times, they won't.
If you had to put money down, which side would you put it on?