That's very interesting, thanks for showing me that, johoe.   I looked up those characters and the smaller one is used almost as a sort of diacritical mark to double the following consonant:

https://en.wikipedia.org/wiki/Sokuon

So it looks to me like you wouldn't expect to sort them in the same order even in japanese localizations.  I wonder if there really is some sort of mistake that was done in the sorting of this text file.  (also, I just learned something cool about japanese orthography, so thanks at least for that you guys!)