We all know these Pokemon (except Spiritomb which are hacked) posses the ability Wonderguard. Wonderguard prevents all damage except super-effective ones. Only Shedinja has Wonderguard legitly and Spiritomb has no weakness so most Pokemon hackers would take advantage of this. There are other ways of inflicting damage and I will list them all below.

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The following are ways of damaging Wonderguard Pokemon:

-Super effective hits (Shedinja: Fire, Rock, Flying, Ghost, Dark type attacks)
-Hail and Sandstorm weather
-Poison, Burn, Confuse, Leech Seed, Curse (Ghost) status
-Stealth Rock, Spike, Toxic Spikes
-Rough Skin, Effect Spore (Poison), Flame Body, Poison Point
-Future Sight, Doom Desire
-Struggle
-Destiny Bond
-Perish Song
-Sleep + Bad Dreams/Nightmare
-Toxic/Flame Orb, Sticky Barb or Black Sludge + Trick combo
-Mold Breaker

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Adding from above, in Mystery Dungeon series:

-Basic Attack (Not the moves)
-Roar and Whirlwind (if pushed to another Pokemon)
-Sticky Items
-Throw Items
-Grimy Food (Burned or Poisoned)
-Traps (Leader and teammate can only activate)
-Walking into the lava
-Hunger (Leader only)
-Orbs (One-Shot, Lob, Hurl, Blowback)
-Future Sight (Fixes Damages)
-Splash
-Vacumm Cut, Wide Slash