It is clearly the result of Woody having no real experience in overseeing the scoring of original music for a film and how it works within the film itself and it also speaks to how Woody wouldn't dare second guess Glass' contributions, even though it probably would've been best to do so sometimes. He says as much in the Lax "Conversations..." book.
Oddly, Woody Allen says almost precisely the opposite in Scott Hicks' documentary about Philip Glass last year. There he claims that the reason he usually doesn't work with composers is that he feels so bad telling them what they've worked so hard on isn't working in the film, but that Philip Glass had no problem at all completely rewriting his cues several times and this made their collaboration much easier than previous experiences.
Digging out my copy of Conversations it appears my memory was focused on this part:
The funny thing is, his music is so riddled with apprehension. I'd say, "This is a casual scene. The music seems to apprehensive." And he'd say, "Oh, no, that's the romantic stuff. The apprehensive stuff I'm saving for the murder." I was thinking, My God, what is going to happen?
He does mention instances where Glass did do some re-writes and, as Woody always is, lavishes praise on him despite having some reservations about the whole thing (as indicated in the above quote, which addresses my criticism of the film's score and the fact that Woody should've spoken up about the music a bit more). He also says that even though he considers Glass a genius, he still prefers working with "the record collection".
Either way - the Glass score failed Woody in that film IMO.