Informatics cause of intra-sample variability, Illumina TruSeq mRNA

[eab]

In an mRNA-seq study using sorted human T cells with libraries prepared by the Illumina TruSeq kit, we noticed that multiple libraries made simultaneously from aliquots of a single cell sample yielded widely divergent results. We believe there may be an informatics issue because many of the species "unique" to 1/2 duplicates appear to be ubiquitously-expressed genes mapping to loci encompassing several possible transcripts. Perhaps a single species is being called one thing from one duplicate library, and something else from the other? If anyone has seen this and has any thoughts, it would be a huge help.
Thanks!