Please see this reply for a description of the known issue: https://biostar.usegalaxy.org/p/20939/
The way to work around this is to run analysis through Tophat, fix the metadata, then proceed with downstream tools. If using a workflow, this means that it should be split into two - one that runs tools through Tophat, and one that runs tools after Tophat. In between the two, correct the metadata as described in the linked post above.
Thanks, Jen, Galaxy team