Maybe you could show us the command you are using?

Also, look into the differences between -g and -G flags. From the manual page:

http://cufflinks.cbcb.umd.edu/manual.html

-G/--GTF Tells Cufflinks to use the supplied reference annotation (a GFF file) to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.

-g/--GTF-guide Tells Cufflinks to use the supplied reference annotation (GFF) to guide RABT assembly. Reference transcripts will be tiled with faux-reads to provide additional information in assembly. Output will include all reference transcripts as well as any novel genes and isoforms that are assembled.

Which one best describes your task?

Thank you Scott Newman ,

So I have to use -G if I want all and only the transcripts in the reference file (GTF).

the difference in the number across different samples is result to the number of new transcripts assembled in each sample.

If you have several samples and you want the new transcripts to correspond across samples, you should also use cuffmerge.