The physical size is irrelevant, it's the strength of the magnet that's the problem, modern permanent magnets are incredibly strong. Feel free to ignore the possibility of the problem, I'm just letting you know of the possibility. Mind you that transmission makers intentionally place a magnet inside the oil/hydraulic pan in order to try to collect the tiny wear particles, if you brushed up against a gear with your magnetic tool there's a modest chance you magnetized a portion of it, which means it'll collect those wear particles just like the intentional magnet in the pan.
Mind you this is not a theory, or my opinion, I have DIRECTLY observed this, simple physical contact with a strong enough magnet WILL magnetize case hardened materials instantly.