I think the main reason is that your application is passed through the hands of multiple non-overlapping parties and the fact that some of these parties have different amounts of information available to them. Typically at the pre-interview stage, your application will go through the hands of multiple screeners that, based solely on what is written, will result in you receiving an interview if you score well. But maybe the folks who vote at the committee meeting will disagree with the screeners on the strength of the written application. The screeners have to sift through a couple thousand applications while the voting committee will only have to go through several hundred, and that allows them to inspect your written application further.
Your faculty interviewer probably meant well. But if the interview was closed file, then they were only really commenting on your fit based on the interview and not on the whole application. Additionally, frequently the faculty interviewer does not actually sit on the voting committee; they write a review and that's it (this was described at 2 of the 3 traditional interviews I had). So as much as they may like you, they won't have the opportunity to come to your defense if there is a disagreement at the meeting. Lastly, it can be difficult to predict how the committee can vote, and they may have just seen similarities between you and other successful applicants. Who knows, but if anyone more knowledgeable of the process would like to chime in, please do.