Can you upload the bnk file instead? The usage instructions says:
Usage: bnkextr filename.bnk
So if you've passed the wav file to the program that could be the reason. Another reason could be that it just doesn't support Metal Gear Rising, judging again by the program description:
Divinity 2: Ego Draconis / Army of Two .BNK extractor
This bnk file only contains the very beginning of the files, the actual majority of the data must be in some other files. They are probably called .wav with some random number like 29373126.wav.