contradiction in cufflinks output

[Hagen]

Dear all,

- my cufflinks (cufflinks v2.0.2) output seems to contradict itself. An example is transcript ENST00000354171.8. There are three exons (all labeled as exon number 1), that all start at the same position, end at different positions though, but all belong to the SAME transcript (which is logically impossible):
nuvol:test htilgner$ cat transcripts.gtf | awk '$4=="1103936" && $1=="chr19" && $3=="exon" && $12=="\"ENST00000354171.8\";"'
chr19 Cufflinks exon 1103936 1104042 1 + . gene_id "CUFF.23504"; transcript_id "ENST00000354171.8"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
chr19 Cufflinks exon 1103936 1104126 1 + . gene_id "CUFF.23504"; transcript_id "ENST00000354171.8"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
chr19 Cufflinks exon 1103936 1106778 1 + . gene_id "CUFF.23504"; transcript_id "ENST00000354171.8"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";
nuvol:test htilgner$

- On top of that there are 11 different "transcript-lines" (lines with the keyword transcript in column 3) referring to the same transcript (when there should be one line and one line only):
nuvol:test htilgner$ cat transcripts.gtf | awk '$3=="transcript" && $12=="\"ENST00000354171.8\";"' | wc -l
11

- the annotation gtf does not have that error
nuvol:test htilgner$ cat gencode.v15.annotation.gtf.Unzipped | awk '$3=="transcript" && $12=="\"ENST00000354171.8\";"' | wc -l
1

- the command line I ran was:
cufflinks -N $myTMPDIR/mapping.bam --min-intron-length 25 -o $myTMPDIR -p 4 -g gencode.v15.annotation.gtf.Unzipped


- Did anyone observe this before ? Is this a known bug ? What should one do ?

Thanks for reading this far!