It's not unusual at all for early cuts of a film to "temp in" commercial music tracks. Sometimes those tracks end up being licensed for the commercial release of the film, sometimes they're replaced with cheaper songs, sometimes the film's composer just imitates them in a non-actionable way.
Nothing So Strange screened noncommercially a couple times with Rage Against The Machine's "Bombtrack" under the opening scene while I tried to get the rights. (Didn't happen. Communists, my ass.) Festivals look the other way at this kind of thing, and it's smart for labels and bands to do the same -- there's no money lost, and if the film gets picked up, then there might actually be money to license the track properly for commercial release. It's really not a big deal to screen a film privately/semi-privately/noncommercially with temp music on the soundtrack. Most of the time, nobody will care.
But you have to be completely idiotic to try to release a film commercially using uncleared music by John Lennon and The Killers. A commercial theatrical release is not a gray area. Damages can be claimed by the copyright owner. Easily. You have to license music for a theatrical release or any other commercial release. I'm pretty sure Yoko Ono and The Killers have lawyers, and I doubt they're afraid to use them.
Fair-use exceptions are possible*, but if the Expelled producers simply used "Imagine" and "All These Things That I've Done" to underscore the emotion of the film's images, which appears to be the case, well, that's not fair use. It's just...use. That's how all movies use music. Fair-use exceptions have to be, you know, exceptional.
These clowns really can't do anything right. Everywhere you look they're screwing up, lying about it, screwing up the lies, and then pretending it all didn't happen. It's a lesson in how not to release a movie to an audience that includes any intelligent people.
Oh, right. Never mind.
But there is a bright side to this. If Yoko sues, it's conceivable that she could win a judgment greater than the entire box-office take of Expelled. That's how absolutely brain-dead and reckless these asshats are. Yoko can sue them for what she would have made them pay originally -- and I'll bet that amount is a lot, possibly in the millions -- plus more for doing it without permission. Plus other stuff. I mean, these guys are screwed.
If I had invested in Expelled or its production company, I'd be getting myself a nasty litigation attorney right now, too. Because this is some world-class incompetence. Of course, I'd also be asking myself why I trusted my money to people who think that the book of Genesis is a scientific theory.
*One fair-use exception possibility would be if you made a movie claiming that the song "Imagine" caused the Holocaust. In this case, you couldn't expect to get permission from the song's copyright owner, but you might need to play parts of the song to illustrate your criticism. This use would not be a normal use of a song in a movie. It would be exceptional. You would at least have an argument from which to start. By the way, you're freaking insane.