There's one side quest in Borderlands 2 that breaks the entire narrative.
For those who haven't played it, the Borderlands universe is run by a bunch of mega-corps. Maliwan, Tediore, Jakobs, etc dominate all aspects of life on Pandora. To add to this, when you die in-game you respawn at a checkpoint thanks to the Hyperion corporation's Renew-U system which resets your body and takes 10% of your cash as the service fee.
Throughout the game you get a bunch of messages and missions from a guy named Handsome Jack. Pretty late in the game, he'll give you a side-quest where he dares you to jump into lava. If you do, then as you respawn he sends you a message laughing at you and gives you a couple of bucks, quest complete.
The issue is that Handsome Jack is the president of Hyperion, and he's the primary antagonist. This means that the head of the company that runs the respawn system, that you're actively working against, doesn't actually disable the respawning system for you, which eventually lets you kill him. Also for some reason he doesn't use his own respawning system. And also Jack kills characters from the first game, who were also attached to the Renew-U system, but I guess now they're not and they're perma-dead.
It's just weird to me because normally I assume 1-Ups or extra lives to be just a gameplay contrivance and it's not a in-universe thing. It's not like Mario is literally dying and resurrecting over and over again, that's just for game purposes. For a game to A) acknowledge that death/respawn is LITERALLY occuring in-universe, and B) it's run by your enemy who DOESN'T disable it or use it against you, is just plain wrong. If there was a mission where you hack into the system and install a backdoor to use it that would be one thing, but as it is it's shining a spotlight on a really weird issue.
And then there's a whole bunch of nonsense with Sirens in Borderlands 3 but everyone acknowledges that the game is shit so whatever.