Checks and counters for Lopunny-Mega
Physically Defensive Pokemon: Lopunny lacks the initial power to break through most of the common physically defensive Pokemon in the tier, including the likes of Mew, Toxapex, Skarmory, Mega Slowbro, and Clefable.
Faster Pokemon: Despite Lopunny's impressive Speed stat, it can't outspeed most Choice Scarf users like Keldeo and Landorus-T, which can force it out with Secret Sword and Earthquake, respectively. Mega Alakazam deserves a mention as well because it naturally outspeeds Lopunny and OHKOes it with Psychic.
Residual Damage: Lopunny is prone to getting worn down by entry hazards, weather, and Rocky Helmet damage, which give it a harder time cleaning and revenge killing late-game because of priority users like Ash-Greninja and Weavile. This also means Lopunny is easier to pick off by weaker attacks like defensive Landorus-T's Earthquake and Celesteela's Heavy Slam.
Likewise, you can get checks and counters to almost every Pokémon through their Smogon analysis.
If we take a look at your team, though, sadly you can't counter it. HO usually doesn't run counters for any Pokémon, you can check them, yes, but not counter. In your team, Tapu Lele is a nice check as it resists High-Jump Kick. If you're very very scared of Lopunny-M (which you should be, it can tear through your team), you can run Scarf Lele, which is pretty nice, too. I'd also recommend Choice Specs Greninja-Ash, as Specs Shuriken, as it does 69 on average to uninvested Lopunny, making it easier for you to pick it off. Outside this, though, you have really limited checks to Lopunny, so you'll have to make some wise predicts, and Lele lead against Lopunny teams work, too.
Hope this helps!