The protocol for RNA seq is different. First, the kit to purified RNA could be bias to genes and not miRNA. Second, normally there is size selection before sequencing that will skip miRNAs. Maybe you can detect precursors, but the expression of the precursors it could not to be correlated to the miRNA expression, and don't know how is the abundance of these compare to the rest of the transcriptome, so maybe the values are low.
You might pick some up, but really, an mRNA-seq experiment is designed to pick up protein coding genes. If you are interested in a detailed look at miRNA expression, it is better to do a dedicated sRNA-seq experiment. As Lorena already mentioned, the protocol is different, and different size selection is applied. I would also use a different sequencing length, and the presence of adapters in the sequence suddenly becomes more of an issue than before.