The possibility for a separate runoff producing an equally close result exists, but it is not probable.
That's not the issue. You're looking at it the wrong way. It doesn't have to be close to begin with. Let's say we use a runoff system. Here's the initial count.
Candidate A: 45%
Candidate B: 30%
Candidate C: 25%
Here, A and B go into a runoff. It turns out that candidate C voters split such that the final result is:
Candidate B: 50.001%
Candidate A: 49.999%
Now we're locked in endless recounts as Candidate A fights to win and everyone is saying how nice it would be if we had just used a plurality system as then the result would have been clear in this case.
More likely the Candidate C voters don't show up for the runoff.