The game will introduce a mechanic to you early on, something perhaps unusual but reasonable in context. Over time, the game will expand from its simpler beginnings. By then, you will be so used to the mechanic that you will rarely pause to notice that it makes absolutely no sense in its new or expanded context.
Example: The Lord of the Rings Online™ uses “morale” instead of health. You don’t die, you just get too disheartened to continue, and you must rally. Sure, goblin spears to the ribs hurt, but you can keep fighting so long as your morale does not flag. A Minstrel’s songs raise your spirits, and you carry on. Then you start meeting trolls, the sort that would crush your skull and limbs with their giant clubs and rocks. You could conceivably rally through a few broken ribs. Then you get to poisoned water that instantly drains all your “morale.” Insta-death from morale drain? Then you get to lava flows, where you burn to death and your armor melts. Life is just a song away!
Example: pills in Left 4 Dead. Reasonable for ignoring scattered cuts and bruises, and then someone starts carving a hole in your chest.
I wanted to use Katamari Damacy as an example, when you start rolling up clouds as if they were huge sheets of plywood and fire that still burns, but Katamari Damacy is sufficiently insane to defy logic anyway. Instead, tell us your favorite example from your current game. Telling riddles to wolves? Backstabbing buildings? Tripping gelatinous cubes?