One further limitation of Bowtie and MAQ is the random assignment of equally well mapped reads to the corresponding genes. Unless, both genes are expressed at a similar level, this procedure will cause wrong expression estimates and should thus avoided.
http://plosone.org/article/info:doi/10.1371/journal.pone.0006323#article1.body1.sec3.p5

The default setting of Bowtie and MAQ is the random assignment of equally good mapped reads to the corresponding genes. Unless, both genes are expressed at a similar level, this setting will cause wrong expression estimates and should thus be deactivated.