People who ranked Begich second still had the vote for their #1 pick counted. It doesn't matter who your #2 pick was if your number #1 pick is still in the race. That's the entire point of picking a #1 candidate.

A vote that is counted in the final contest of an election is not a vote "thrown away" even though the person they voted for lost. Voters have to be allowed to pick a candidate who ultimately doesn't have enough supporters to win an election. That's how elections work.