Every microRNA (miR) gene that I have seen mapped to the genome - in mouse or human (or other species) - maps either within an intron of a protein-coding gene or as a distinct transcription unit outside of any other gene. Thus, I would not expect to find any miRs mapping to exons.
The question is a bit unclear to me, so I am guessing here. If you have sequence reads and need to map these as within exons, then they should map to the RefSeq mRNAs. Also, see Jeremy's response.