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I've noticed that Shedinja is a gimmick but an interesting one (and devious combined with Soak). However, throughout my searching the only counter I've seen is Prankster Whimsicott with Worry Seed. Are there any others that I'm missing?

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Shedinja would see a heck of a lot more use if that was its only counter.
@Fizz - Could this be like a thread since different people could have their own counters/methods? I'm not saying that I want this to be a thread, I'm just asking if this question is already a thread.

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First, wonder guard Pokemon can be damaged by super effective attacks.

Things that can change or suppress abilities can stop Shedinja. If you're playing competitive battles, then I think the best way to do this is mold breaker. You can also use mold breaker to restore some kinds of expired food.

Shedinja has exactly 1 HP, so anything that deals damage without attacking will "one-shot" Shedinja. Good ways to deal this kind of damage include stealth rock, spikes, poisoning, burning, leech seed, and sand stream.

source: a lot of Bulbapedia pages (I can provide links if you want)

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Also, Sturdy Shash is something too sumwun
It is very hard to get sturdy on Shedninja; by the time it takes to setup, your opponent would have KO'd at least Shedninja. Any type of indirect damage (like Entry Hazards/Status) KO's Shedninja even if it holds a Sash. :P
You forgot to mention how Reshiram can use it's Turboblaze, or Zekrom's Teravolt. And Solgaleo/Necrozma can use Sunsteel Strike/Photon Geyser. You also forgot to mention Hail, Rough Skin, Poison Point/Touch, Iron Barbs, and Flame Body. A Shedninja with Sturdy may be hard to get (unless you're in Showdown's Balanced Hackmons format), but Focus Sash Shedninjas can still be a thing.

Be sure not to tell me to make my own answer.
The things in my answer were examples, not complete lists. Also, Shedinja is immune to photon geyser.
@sumwun - At least my comment can give people extra info. Photon Geyser ignores Wonder Guard so Shedinja isn't safe. And if I'm wrong (I believe I'm not), does this mean Showdown is glitching?: https://replay.pokemonshowdown.com/gen7anythinggoes-825729143
Oh. I thought the only weird thing about it was becoming physical if the user had higher physical attack.