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For example in Gen 6, Clamperl can learn Shell Smash while Gorebyss cannot

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Fyi, all of this information is on the site, if you go to the move page for each Pokemon, there will be a category for this
I can do it, but it will take a while, and it probably won't include the Gens that the move was in due to the character limit. Is that alright?
I recommend that you don't attempt to answer this question manually. To answer it accurately and completely, you would need to check hundereds of dex pages and repeat the process for every generation. There are much better uses of your time.
This question is a scripting project for whoever cares enough.
The list goes on and on but the only one I think is noticeable is Shroomish which learns spore at level 40, a move Breloom cannot learn by level up

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Here is a list for Scarlet and Violet

  • Annihilape - Covet
  • Azumarill - Splash
  • Banette - Astonish
  • Breloom - Spore
  • Camerupt - Double-Edge
  • Crabominable - Vise Grip; Payback; Crabhammer
  • Donphan - Tackle; Flail; Last Resort; Doubleedge
  • Eelektross - Spark; Bind; Tackle
  • Floatzel - Tackle
  • Florges - Vine Whip; Tackle; Fairy Wind; Razor Leaf
  • Froslass - Weather Ball
  • Garganacl - Smack Down
  • Goodra - Acid Armor
  • Grafaiai - Bite
  • Grumpig - Growl
  • Honchkrow - Peck; Gust; Assurance; Mean Look; Torment
  • Kricketune - Bug Bite
  • Masquerain - Bubble Beam; Mist; Haze; Sticky Web
  • Mismagius - Confusion; Mean Look; Hex; Pain Split; Payback; Perish Song
  • Raichu - Fly
  • Skeledirge - Yawn
  • Slaking - Focus Energy; Uproar; Fury Swipes 14, Focus Punch; Headbutt
  • Sunflora - Endeavor; Synthesis
  • Swalot - Pain Split
  • Ursaring - Babydoll Eyes
  • Vivillon - Harden; Tackle; String Shot; Bug Bite
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You're missing a lot of the TMs (raichu doesnt have fake tears but pikachu does, slowking does not have helping hand but slowpoke does)

There's too many of these to list in one comment.