Hello @Loc_Le
Yes, this tool is a bit tricky to use. A full adjustment at the tool wrapper level is pending but for now, the solution is to include .gff on the collection identifiers.
You can recreate the collection (retaining the file extensions) or use the Extract Element identifiers, text editing tools, then Relabel identifiers functions to add these back in. And, for HTP use cases, Apply Rules can make this sort of adjustment too.
Recreating the collection is the easiest, so try that first if this seems overly complicated.
Hope this helps and follow up questions are welcome! 