Question about output

[KrystalTW]

I have been using AssemblyImprover following VelvetOptimizer for 36 bacterial genomes. For the majority of the genomes, I generated the expected output files:
contigs.fa.scaffolded.filtered
contigs.fa.scaffolded.gapfilled.filtered
scaffolds.scaffolded.gapfilled.length_filtered.fa
scaffolds.scaffolded.gapfilled.length_filtered.sorted.fa

But for a handful, I get the following files:
contigs.scaffolded.fa
contigs.scaffolded.gapfilled.fa
scaffolds.scaffolded.gapfilled.length_filtered.fa
scaffolds.scaffolded.gapfilled.length_filtered.sorted.fa

What is the difference? Are these unexpected files usable? I can not find any documentation about this discrepancy anywhere, so anything you can tell me would be helpful.