A lot of times the CD design information goes to an art department at the same time as the band is recording. The vocalist may decide while laying down his vocal tracks that it sounds better with lyrics a different way, or with certain words omitted, etc. Sometimes they are wise enough to get the art department the updated version, or maybe the art has already gone to the printing press and the ink plates have been made ($) etc. Lots of things like that play into the discrepancies.