Yeah, if I was responsible for the actual conversion I'd definitely look into it. I would expect the main reason for this being either 1) some of the files are extracted incorrectly, 2) the files are similar to what vgmstream can handle, but some have extra bits that it doesn't recognise. The latter is most likely, since some formats have variations that are similar, but not always exactly the same. It could also just be some weird bug in the code, it's an open-source project that gets built every time the code changes, so it's not the most stable thing in the world.
EDIT: Question for Mystie: what platform is the Cel Damage file from?
EDIT: Question for Mystie: what platform is the Cel Damage file from?