Two possible incorrect alignments of spliced reads. 1) A read extending a few bases into the flanking exon can be aligned to the intron instead of the exon. 2) A read spanning multiple exons from genes with processed pseudogene copies can be aligned to the pseudogene copies instead of the gene from which it originates.
Kim et al. Genome Biology 2013 14:R36 doi:10.1186/gb-2013-14-4-r36