Why does Pandora keep playing Incubus when it should know I hate it

The Pandora algorithm, in an overly simplified explanation, uses a weighted system on various attributes of your music to determine what you most prefer to hear. When assessing a song on one of your stations, try to compare this specific song to all of the qualities you want your custom station to embody. If you feel this song meets a large enough number of those qualities then you should "Thumbs Up" it. Pandora then adds extra weight behind ALL of the attributes of that song (whether they were exactly what you wanted or not).

Sometimes an upbeat song is what I'm looking for, but because it's also atonal, in a minor key, has a swing rhythm, has a male voice, and harmonized backup vocals (all of which I am trying to avoid) it would be more helpful to "Thumbs Down" on this song instead. If I had done the opposite, I would now get MUCH more of those qualities in addition to the upbeat quality which I originally liked.

Over the long term, your preferred weighting will work itself out but for something as detailed as song length, I think you'll find Pandora will not be able to zero in on that attribute specifically.

(These are my unresearched observations from using Pandora over the past several years.)

No, Pandora does not go out of its way to not play that song. The explanation is simpler - Pandora can play only songs for which it has distribution rights. For some songs it does not have the rights (usually because of the pricing for the particular song), so while it will create a radio station with similar music, it might never get to play that particular song.