Well, I don't think that the EA team doesn't notice these details but they would have to have the band come in again to record the songs in the studio. I think the minimum fight song assigned to a team is one (user created teams), but no more than three.
For example, USC's fight song, "Fight On!" has 2 versions in the game- a short version that is played after a touchdown, then a longer version after the PAT. Then there's "Tribute To Troy" (added in a later version of the game, I started to notice it on 2005 or 06) that is played on defensive plays but I noticed they also still incorrectly play it on 1st Downs when the team is on offense. It should be an even shorter version of "Fight On!" for first downs.
They also messed up UCLA's fight song for the longest time. I only know this because my brother-in-law and I would play and whenever he scored a TD in the earlier versions of the game, he'd be dumbfounded as to why that was. EA finally corrected this, I believe in the 2003 or 2004 version of the game, to which my brother-in-law rejoiced in happiness. EA must have recorded that song again.
They used the University of Notre Dame Marching Band for all their band music. Check our the credits. None of the music heard in the game came from their respective university's band, believe it or not!