The FBgn0031208 gene has 5 exons in the original annotation file (i.e. Drosophila_melanogaster.BDGP5.25.62.chr.gtf)
and only 4 counting bins in the flattened one (i.e. Drosophila_melanogaster.BDGP5.25.62.chr_dexseq_noaggregate.gff).
Following inspection of the annotated transcripts in Ensembl 62, we can explain how the initial exons break down into 4 different counting bins.