The name of the save file makes a difference.
sav.dat means VC, and any other name means Emu/cart
Your Cloyster is illegal; ie: while the moveset was valid for tradeback, you didn't actually perform the trade.
hint: Location data is wiped when traded to Gen I.
As for the Raikou, let's just say PKHeX hasn't added it to the checks.
Since you used our file, you know of it's legality status, so overlook it.
Given for the most part you made a mistake and it isn't a bug, I'm locking this thread.