Before we go any further, most of what follows has no basis in canon, and is my speculation. I know of no examples in canon that fit either description.
Let’s start with spells that fail on Muggles. We can guess that any spell in this category would affect a wizard/witch’s magical faculties, so anything to impair or interfere with your magic. Some examples that might be possible:
An Anti-Disapparition Jinx might fail silently. Since Muggles can’t disapparate, the jinx would have no effect on them. That said, if a wizard/witch tries to take a Muggle along by Side-Along Apparition while they’re under this jinx, what happens? Discuss.
I think a Shield Charm would have limited to no effect. It’s clearly designed to deflect spells, but Muggles don’t use spells to attack. Perhaps a physical invasion (bullets, soldiers or a punch in the face) wouldn’t be stopped by a Shield Charm. Whether this falls into the category is debatable, though. It would probably have a similarly negligible effect on an assailant who wasn’t casting a spell. (Also, I’m sure any wizard worth their salt could stop a physical attack, just not with this charm. I know this happens in the films. Films != canon.)
And finally we come to my first bit of “genuine” fact: Muggles can’t brew potions. Brewing a potion involves more than just stirring a cauldron; it needs magic too. Of course, this isn’t a spell, more a magical discipline, but I include it for interest. From a 2006 interview with JKR:
Can muggles brew potions if they follow the exact instructions and they have all of the ingredients?
JKR: Well, I'd have to say no, because there is always... there are magical component in the potion, not just the ingredients. So, at some point they will have to use a wand.
That’s all I can think of on this front, so let’s see if there are any examples of magic that affect Muggles, but not magicians. Let’s tackle the Muggle-Repelling Charm, because I think it’s important.
Muggle-Repelling Charms seem like an obvious fit, but perhaps not. We can guess that the protective charms Hermione casts in Book 7 are to keep away Muggles, but presumably they want to keep away other magical beings, too? (See: Death Eaters.) I think it’s questionable whether these charms actually target non-magical people by default, or have been cleverly tuned to be that way. I don’t know whether these might fall into your category of “extra effort”.
Let me now blow a hole in that theory. The concealment of the magical world extends beyond Muggle-Repelling Charms (at least how they’ve been described: we remember an urgent appointment, or see a derelict castle). Consider people disappearing off the street to St. Mungo’s, the Leaky Cauldron’s apparently invisible front door, or the barrier at Platform 9¾. The filters that hide the wizarding world from magical view seem to extend beyond these simple charms.
And to volley that point one final time, it seems more a matter of perception that a hard barrier. Lots of Muggles (such as Hermione’s parents) interact with the magical world, despite these stops put in place. Perhaps you don’t notice them unless you know that they’re there. So if somebody who doesn’t know about the Leaky Cauldron walks past it, they might ignore it. (Like an extended version of the Fidelius Charm).
Otherwise, nothing concrete springs to mind. Possibly there’s something significant in the way Muggle technology is mostly screwed up around very magical areas, but again, I don’t think that’s targeted at Muggles, but just a general effect. Indeed, Hermione in Book 4:
“All those substitutes for magic Muggles use — electricity, and computers and radar and all those things - they all go haywire around Hogwarts, there's too much magic in the air.”
So I don’t know if there’s any concrete example I can think of for a spell that affects a Muggle, not a magical being, that definitely isn’t that way by design.