Well, it's not like if it can't be in troubling situations: against Ghost types all it could do is spamming Ancient Power, as its other attacks don't work on Ghost types. Steel types as well could be problematic as all of its attacks are not very effective on them, same for Rock types, excluding Ancient Power. To say: I think it would have very low chances against Roy's Mega Lucario. It resists to all of its attacks, and has type advantage, so with Close Combat it would demolish it. So as much strong Pagogo is, it doesn't mean it's always a "one shot mon", there are situations in which it does have its limits (only if it uses the Stellar Form it would be invincible, but it will never use it in regular battles. Also keep in your mind that in its last battle, in order to land that powerful Tera Starstorm, she made Pagogo boost its stats by spamming Ancient Power first, so in order to really be "one shot" it has to land Ancient Power in hope that it boosts its stats). Which is why there are Liko's other Pokemon to compensate those (Meowscarada greatly counters Ghost and Rock types, and an eventual Armarouge would demolish Steel Types). The thing with Liko's current team, is that if Hattrem and Charcadet evolve, she will be a colossal amount of type coverage: where one Pokemon is weak, the other is strong, and together they're a formidable team... it's the story of the life of Pokémon battling in general. Once all Liko's Pokemon evolve, she will have a BEAST of a team.
Even so thought, there would still a bunch type combos that would give trouble to Liko's team anyway and... ironically enough (and not in a good way) Roy himself in future will have a Pokémon that would be problematic for Liko's whole team, if they ever fight again: Skeledirge. Because a Fire-Ghost type is dangerous for all of Liko's Pokemon.
