Yes, different chromosome naming schemes will lead to poor assignments. Why? Because the tool is matching up coordinates on chromosomes between the BAM file and the reference annotation file.
Then for this, it sounds like this change didn’t full resolve the discrepancy between the reference genome (fasta) and the reference annotation (GTF, GFF3).
The tool is having trouble parsing the data but it is hard to guess why.
Do you want to post more details about your reference data? Which genome, which annotation file, and the changes you made. Maybe we can come up with a working strategy.
These are some guides if you want to explore this more on your own, too.
- FAQ: Mismatched Chromosome identifiers and how to avoid them
- FAQ: Extended Help for Differential Expression Analysis Tools
- Reference genomes at public Galaxy servers: GRCh38/hg38 example
Great that you were able to notice the problem and try a fix! We can probably help to get this working. 