samtools / bamUtil | Meaning of  as Reference Name
As per the SAM/BAM format specifications:


  "RNAME: Reference sequence NAME of the alignment. If @SQheader lines are present, RNAME(if not ‘*’) must be present in one of the SQ-SN tag. An unmapped segment without coordinate has a ‘*’ at this field.  However, an unmapped segment may also have an ordinary coordinate such that it can be placed at a desired position after sorting.  If RNAME is ‘*’, no assumptions can be made about POS and CIGAR." -- http://samtools.github.io/hts-specs/SAMv1.pdf, emphasis mine


So, yes, these are the unmapped reads. 

I haven't used this splitChromosome utility before myself, but as it splits the BAM file into one BAM file per chromosome, I suspect it simply also creates a BAM file for the unknown (*) chromosome. Why the numbers don't match I can't tell.

How to deal with that file in your pipeline will depend on what the pipeline is meant to do. But if you aren't interested in these reads, I suppose you could simply remove it before continuing to the next step.