If Tonberries and Cactuars the party fights in FFVIII do not include the ones that chocobo knows in the mini-game, then there's no contradiction. I would assume the bulk of Cactaurs and Tonberries do not know chocobo personally.
Unless the Cactuar and Tonberry in the mini-game specifically appear in FFVIII as well, like say Jumbo Cactuar and Tonberry King. |