missing transcripts in both tracking and combined.gtf

[MaissaNabil]

I had multiple gtfs from different samples and I was trying to merge them using gtffcompare "without providing a reference". The resulting tracking and combined.gtf files are missing some transcripts from each sample. Close examination revealed that gffcompare is discarding these transcripts from samples when there is another transcript is present with the same intron chain in the sample.
I did not use the -D option "so even if these transcripts were redundant they shouldn't be discarded" my command was simple :

gffcompare -o union_out *.gtf

why is this happening? and is there away to include these transcripts in my tracking and combined.gtf?