A Rogue Pokémon is a term coined for a group of Pokémon species that are usually found to be antagonistic to people of their own merit, or usually teaming up with villanous teams.
The term was coined by Professor Magnolia, in that usually, some people or teams may pollute the idealism of humans to a Pokémon species, which filters through the species in large numbers across regions or even the world. While it doesn't mean the whole species is antagonistic, those Pokémon are often seem to be stereotyped into the same category. Similarly, this maybe through the species itself and its feelings towards how its treated by humans, or fellow Pokémon alike. These Pokémon are wild, making their actions their own and not of that of a Trainers. While Trainers may influence this, they differ from Pokémon used by villanous people.
As stated in her research, Professor Magnolia reiterates that these species are not inherintly evil or antagonistic as a whole, but due to different situations or personality traits within them, it occurs to a majority percentage to the species, which is what gives them the status as a Rogue Species.