Problems with analysis of small RNAseq data - Adapter trimming
I would first recommend you ask this question biostar as the subject matter you are inquiring about is much more relevant there.

That having been said, you have another option which is to use an aligner that soft clips 3' ends of reads specifically to account for adapter (or polyA, or whatever) contamination that might have flew under your radar.

STAR is such an aligner. If you search their mailing list archives for "clip", you should find several posts related to your question.