That’s a thing in some stories and plenty of games, but I don’t quite understand it, especially in a setting like MLP. Spells and magic seem to just work when affecting any creature. Any thoughts or explanations?

7948195
It's prevent the "Wizard" from solving every problem, as such allowing a story to exist.

7948195
Usually it's some form of built in resistance to certain types of magic, usually something developed or engineered. Or said resistance is a type of magic in and of itself

7948195
In my headcanon the magic which infuses ponies' every cell gives them an inherent resistance, because magic of different "wavelengths" inherently eats away at each other. So it's very difficult to cast a spell on a pony, or transform them, in a way that lasts long-term - particularly with unicorn magic, other kinds being more variable. (This limits healing magic to first aid, and the general principle is also what makes group casting an utter pain.)

Now, as for a more general resistance/immunity, there may also be creatures like that - the big worm Twilight and Cadance fought that time seemed fairly resilient against their powers, and indeed "high-level" beings in general might be. (I doubt pre-alicorn Twilight could just turn Celestia into a potted plant.) But a lot of this is speculation and inference, of course.

7948195
I use it for storytelling purposes.

Yes, I could just use Celestia's control of the sun or Discord's chaos magic to solve literally every problem in Equestria. But stories where there's no problem to solve; no conflict to resolve are boring. They're boring to write, they're boring to read, they're boring to play out on video games.

Think of Scootaloo telling her ghost story on the camping trip.

Okay, so maybe this wasn't about magic resistance as much as me resisting the use of magic to solve problems, but the other responders are right: When there's a solution that works 100% of the time, you're always going to use it. If you want people to explore other avenues, it has to be just as viable.

7948195
Maybe it's like being Fire proff

or magic only ones one other that also have magic

maybe their body it's has Magic resistant DNA

MAGIC and all of that
MAGIC in fantasy, soft magic vs hard magic

edit:

7948432
I have something similar in my setting: The Holy Light which is a completely different Magic System from Magic in that instead of utilizing arcane knowledge and power, Holy Light is fueled by ones' own Belief and emotions. Holy Light is also different in that it serves as an "Anti-Magic" of sorts that Magic cannot touch and is often destroyed upon coming into contact with it; and that Holy is strongest during the Daytime and in the presence of The Sun. Unlike with Magic which is cast silently, Holy often employs Chanting to cast its' abilities and is further strengthened by the Casters' own Charisma: which serves a dual purpose to empower the Casters' spell through their own determination and to demoralize their Enemy to weaken them through the presence and sureness of the Casters' abilities. Ultimately, the strength of Holy is determined by ones' own will and if they believe that their actions are a step towards making the world around them a better place from it.
If you feel doubt or fear or guilt over the actions you are about to take or are taking; the Holy Lights' power within the Caster will weaken and the spell they are conjuring from it will do nothing. But if you are determined, courageous, and devoted to the task; than you'll pass the vibe-check.

Active knowledge about the Holy Light had waned in recent millennia in Equestria; through the conceited efforts of Unicorn Nobles who wish to subjugate all Tribes under their hooves and to rule unopposed through a puppet Princess, however even within Equestria there are those who still believe and follow the teachings of The Holy Light.

The Crystal Ponies use The Holy Light throughout their everyday lives, holding to a belief known as The Prismatic Cycle: which dictates that all Crystal Ponies are one part of a great machine that was made by a God of Knowledge and Mathematics that created their bodies as crystalline vessels to house The Holy Light that he sends out into the world to experience life through, and that a Crystal Ponies' soul would return to The Grand Prism upon their death in order deliver their accumulated knowledge and experiences to it with the goal of perfecting their Gods' macroscopic understanding of life and create new knowledge for future generations. Upon ones' return to The Grand Prism; a Crystal Pony can approach their God and be offered a choice to be Reset and returned to the living world again to continue the cycle within a new body carved for them.

7948195
'Magic' in the broad sense is almost arbitrarily powerful, Giving characters access to an arbitrarily powerful force tends to end in said characters just 'nope'ing the entire plot, which is boring. Therefore magic requires limitations, the mage can't just vanish the Big Bad, because magic does not work like that.

Magic resistance is one of the most common limitations that is used, the mage can't newtify anyone she wants because the innate magic of a pony wants to remain a pony and not a newt (or whatever other justification the author wants to give). That said, it is magic resistance and not immunity, a powerful caster can overpower the resistance and force the pony to become a newt regardless.

7953659
Eh, that's anti-magic not magic resistance, a completely different thing.