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Probably because it either didn't know or simply forgot that Seismitoad is a Ground-type. It's not the Pokemon's job to remember the type-combinations of every single Pokemon out there or how the type chart works. That's... what the trainer's for. If this was Ash commanding Pikachu to use an...

It doesn't seem like Pikachu disliked Gou, it was simply rushing into action on its own before waiting for Gou's orders, with Gou remarking that Pikachu's actions remind him of Ash.