How to defeat an active Digglet Pokemon when oppenent has an additional on bench
Diglett card from XY - Evolutions expansion has an interesting ability:


  Ability: Submerge
  As long as this Pokémon is on your Bench, prevent all damage done to this Pokémon by attacks (both yours and your opponent's).


The phrase this Pokémon is special in Pokémon TCG - it refers to this one and only particular Pokémon, not any other, not even other Pokémon of the same species.

Thus it's quite simple to defeat two Digletts, because the active one can be damaged without problems. Just knock out the first one during one turn, then the second one during later turn.