That might be part of it, yes. Some Pokémon are also just notoriously badly-behaved. I have several that I've been working with for months now that are still difficult, and I've heard that's something common in Gyarados.
However if you think it might be nursing a grudge for past treatment my advice would be to open a dialogue with it. Pokémon are not animals. They are intelligent beings, and treating them like people goes a long way toward earning their respect.
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However if you think it might be nursing a grudge for past treatment my advice would be to open a dialogue with it. Pokémon are not animals. They are intelligent beings, and treating them like people goes a long way toward earning their respect.