In the case of an ambiguous match Bowtie and MAQ randomly assign reads to one of the targets, which results in a higher proportion of incorrectly mapped reads (Figures 2C, 2E). Hence, neither Bowtie nor MAQ should be used for mapping reads to quantify gene expression.
http://plosone.org/article/info:doi/10.1371/journal.pone.0006323#article1.body1.sec2.p5

In the case of an ambiguous match Bowtie and MAQ randomly assign by default reads to one of the targets, which results in a higher proportion of incorrectly mapped reads (Figures 2C, 2E).