Double check your inputs. Specifically for this problem, start by checking that the GTF file contains gene_id and transcript_id attributes (ideally, these would be distinct values) and that the genome build the GTF is based on is not a mismatch for the genome build mapped against with HISAT2 (check the chromosome identifiers).
FAQs that explain how to do the above: https://galaxyproject.org/support/#troubleshooting
Related prior Q&A (others are in the far right, or can be searched by keyword): https://biostar.usegalaxy.org/p/24210/
Thanks, Jen, Galaxy team