Some Pokémon have attacks that hit Benched Pokémon, either instead of or in addition to the Defending Pokémon. These attacks are useful for a few reasons:
In the early-game, they let you hold off taking Prizes and turning on your opponent's comeback cards, while still counting as a form of progress.
In the late-game, you can go after dead weights sitting on the Bench, like a Jirachi that's already served its purpose, for the final Prize.
You won't care if your opponent puts a Pokémon that resists or is immune to your attacker in their Active Spot, because you can go after their Bench instead.
Some decks can utilize a "7 Prize" strategy by throwing 2 ex's and 1 non-ex (in any order) at you, followed by one final ex, negating the 2-prize drawback of their last ex. If you have a Bench attacker, you can go straight for the ex's on their Bench when they have their non-ex out.
You can go after Pokémon with 0 Retreat Cost, like Pidgeot. In contrast, forcing these Pokémon to the Active Spot is ineffective, as you will get one attack off and they will just retreat (unless said attack 1HKOs them!).
If the Defending Pokémon is a dead weight, you force your opponent to spend resources (be it Energy to retreat, switch cards, or Swoop) to get it out of there. They cannot rely on you to KO it for them, and if they do nothing, you'll just continue sniping their Bench.
Below are some commonly seen Pokémon with attacks that hit the Bench.
An optional tech for decks with Bench attackers is Ancient Technical Machine [Rock]. After spreading damage to the opponent's Bench, you use ATM Rock to devolve their Pokémon, reducing their max HP, scoring multiple KOs at once. This can be helpful against high HP Evolved ex's, though you will only take 1 Prize against them.
Remember: ATM Rock can only be attached to Evolved, non-ex, non-Owner's Pokémon.
These are the most direct counters to Bench attackers.
Dugtrio only protects against damage, not effects that place damage counters (like Dragonite ex δ's Dragon Roar), nor effects that force switch-ins.
Dugtrio has a decent attack if you can get the Energy on it. 60 damage is enough to 1HKO Dark Tyranitar after Weakness.
Some softer, but nevertheless effective counters can be found in the DPS checks section.