In 2014, I claim to have seen a report of Charap being marked as Japanese in origin. I cannot remember where I saw this, but I do remember seeing it.
A few days ago, Bethany Lieflijk (one of my Twitter followers) reported that her Gaspar had become Japanese in origin after being transferred.
I also found this GameFAQs thread where several users report the same thing happening to Kazza and Gaspar.
My hypothesis is that the bug has something to do with in-game trade Pokémon having special language flags due to Foppa being specifically German.
EDIT: Apparently this issue also occurs in Generation V, so it's not a bug in Poké Transporter. It's much harder to notice in Generation V though.
EDIT 2: theSlayer checked, and apparently Charap, Kazza, and Gaspar are all flagged as Japanese in origin in English Diamond and Pearl. This seems to be fixed in other languages (Japanese is clearly fine, French and Korean were checked) as well as in Platinum (despite one of the sources I found claiming they had the same issue with in-game trades originating in Platinum).