As pointed out by Mark Brown in his latest Game Maker's Toolkit video, Warner Bros. Interactive have applied for a patent on the nemesis system used in Shadow of Mordor and its sequel, Shadow of War—the system that personalizes orc NPCs in response to actions players take against them. Specifically, it's a patent for "Nemesis characters, nemesis forts, social vendettas and followers in computer games". Brown compares it to the patented floating arrow that told players where to go in Crazy Taxi, which was part of the lawsuit Sega filed against Fox Interactive in 2003, after The Simpsons: Road Rage used the same mechanic. (The suit was settled out of court for an undisclosed amount.)
However, other games have used mechanics similar to the nemesis system since it was established in Shadow of Mordor. Warframe, Assassin's Creed Odyssey, Path of Exile's Betrayal expansion, and the War of the Chosen expansion for XCOM 2, for instance. Perhaps that's because the nemesis patent is currently listed as "Pending", though a look at the timeline of legal events shows that after being rejected in 2019, it was re-examined in 2020 and then progressed to the "notice of allowance" stage—meaning that if the paperwork and fees are filed in time, a final patent will be issued.
That said, simply owning a patent on a videogame system isn't the same as preventing anything similar from ever being made. Sega's dispute with Fox Interactive involved more similarities between the two games than just the floating arrows, and while Microsoft have had a patent on games awarding bonus points "if the player performs feats of style that are not necessary tasks of the game" for 19 years, as far as I know they've never enforced it on the many games with style points—the patent was filed to protect Project Gotham Racing's kudos points specifically. Likewise, Bandai Namco's patent on "arranging a plurality of objects" in the Katamari Damacy fashion didn't prevent The Wonderful End of the World, Anarcute, or Donut County from exploring overlapping ideas, and EA's patent on the BioWare dialogue wheel, granted in late 2011, didn't shut down Deus Ex: Mankind Divided or Fallout 4.
One software patent that was used to target videogames broadly was the Uniloc Corporation's patent on the concept of product activation, which was dubbed an act of "patent trolling" after being used in an infringement suit against Microsoft. It was eventually eliminated after Sega, Ubisoft, Cambium Learning Group, and Perfect World Entertainment filed a case against it.
The long and the short of it is that, yes, Warner Bros. Interactive did file a patent on the nemesis system, but that isn't necessarily the reason we haven't seen more games use it. Nintendo have had a patent on sanity systems since they published Eternal Darkness, yet we've seen equivalents in Don't Starve, the Amnesia games, Tokyo Dark, Knock-Knock, World of Horror, and others. While Namco's infamous patent on loading-screen minigames might have put a few people off the idea, it didn't prevent The Sims 3 or Splatoon from having them. The nemesis-inspired game Ken Levine's Ghost Story Games studio is working on will probably be fine, and maybe someday we'll get the Moby-Dick game with nemesis whales we've been waiting for.
Recently Bloober Team patented The Medium's Method of simultaneous playing in single-player video games.
(If you've spent this whole post confused because you didn't think videogame mechanics could be patented, you're actually thinking of copyright.)