I don't believe it was lip synced. The vocals were live from everything I've read. The instruments were pre-recorded as Flea says. It's what you sign up for when doing the superbowl halftime show nowadays.
The reason the audio company for the shows gives is simply they do not have time to sound check everything in the 3 1/2 minutes they have to get going. So vocals to canned track is the only way they have gone for about two decades. That includes, for the most part, the national anthems. Often the vocals have a track they can sing over or chose not to so that is often even canned. The Black Eyed Peas likely should have used the canned vocal route instead of trying to sing live.....
http://www.utsandiego.com/news/2014/...-mostly-mimed/
As mentioned most awards shows do the same thing and heck as we all know many hip hop/pop acts use completely pre-recorded vocals for a good chunk of their concerts with a few notable exceptions (Pink being one who's mic is always live...for good or bad).