Hard for me to say without knowing the examples. Perhaps the song “Sabotage” was also in the soundtrack for that movie? Or perhaps that’s a form of advertising that didn’t meet Yauch’s definition, because a film is also a sold work of art?
Also, independent films can often use music without permission, and not pay for licensing unless and until they actually get picked up by a distributor. So it’s possible you saw trailers that the Beastie Boys didn’t even authorize.