This most likely means that you did not have the extra attributes included in your reference annotation file (GTF or GFF3) provided to Cufflinks and/or CuffMerge in an upstream step.
The tss_id and p_id attributes are factors here. Including gene_id will include the common gene name in the output, if provided in the annotation.
The Cufflinks web site has versions of annotation files with these attributes included for many common model organisms. Be sure to use the UCSC version, if using the same reference genome in Galaxy: http://cufflinks.cbcb.umd.edu/igenomes.html
There can be other causes, that include genome mismatch problems (identifiers that do not match) but these result in other symptoms along with this one. If you think this may be a cause, the wiki help here can help:
Hopefully these resources help to diagnose your specific issue,
Jen, Galaxy team