I opened my PBR save file in the most recent version of PKHex, and I find a duplicate of a Wailord I had in my PC box in the fifth slot of my party, instead of my Gastrodon (East) (Nickname: Katsuraio).
EDIT: Nevermind, I realize that PKHex only checks your most prominent Battle Pass team, rather than your actual party Pokemon from Diamond/Pearl. So the only thing I can suggest is to make that clear, so no one gets worried.
PbrSaveData