It is common in basketball and football to be slightly ranked below a team you've beaten by just the way the schedules and wins and losses work out. I know under the covers how Virginia Tech has skipped most of their most difficult games and have lost to nearly all the ones they kept. But it is what it is. They finished 3rd in the ACC. Nobody in the entire conference had fewer overall losses than Virginia Tech. Only 6 teams out of the top 25 have fewer losses than Virginia Tech. The #2 team in the entire country has 6 losses. So I can certainly see why they're ranked there.
Fewer losses is an odd metric for VT because they played so few games. In the ACC, their 9 wins is 6th most and is tied with 3 other teams that also had 9 ACC wins. In other words, they had more ACC wins than only 6 of the 15 ACC teams. Combine that with having the 15th! rated strength of schedule in the ACC and one has to ask, what did they actually accomplish to earn their seed apart from just cancelling games against the hard teams?