Hitokage/Charmander, Lapras, Hikozaru/Chimchar, Pokabu/Tepig). It's not a HUGE problem, nowhere near as widespread as N was lead to believe, but it is one that exists and Satoshi is definitely against! Besides, he's also always fighting the Rockets when he runs into them trying to capture/steal Pokemon and they're definitely common too! Poachers too and Hunter J... it's more believable if we count Pokemon otherwise betrayed by humans in that catagory, not just being abandoned by their trainers, I think.
But I guess that'd be heading into theory/headcanon territory, huh? ^o^;