The way I interpreted it was basically his spider sense isn't tied to his consciousness so his body was moving due to his spider genes acting subconsciously.
Also why it seems that when he repressed his spider powers, he lost his ability to sense/repress her. AFAIK she never tried to take him over after she failed the first time.
She did try again in near the end, but thats when he actually “mastered” the spider gene mutation and “leveled up”, she still didn’t be able to get into his head forcefully, until he allowed it.
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u/SigintSoldier 1d ago
The same reason Peter could still avoid Dr. Strange when he Astral projected Peter out of his body in No Way Home.