A character that is explicitly science-fiction deals with a fantasy/magic-using villain of some kind. Not "technology that is so advanced it looks like magic." 

***1). Superman:***  
^(TLDR: Superman (and alien) fights wizards.) 

* Superman and Captain Marvel (Shazam) have different stat builds. Superman has maxed physical attack, physical defense, and speed. But he has the "special defense" of normal person and no magical output whatsoever. 
* So, if Superman gets hit by "spell that turns you into a carrot" he's just as screwed as any other mortal. Of course, you'd have to hit him with it first. But the threat remains.  
* Magical superheroes, such as Wonder Woman or Captain Marvel, are explicitly resistant to magical attacks. So, "spell that turns you into a carrot" might bounce right off them. 
* In *Superman/Shazam: First Thunder*, Clark bemoans the use of magic by mercenaries. So, he's thrilled to befriend the magic-resistant Captain Marvel. Until >!he finds out he's 10. !<

***2). Ben 10:***   
^(TLDR: Ben (who has alien technology) occasionally fights sorcerers.) 

* Ben's anatomy fuses to a piece of alien technology. This "Omnitrix" allows him to transform into various alien species. 
* But magic exists across the galaxy. So, he naturally comes into conflict with magic-using criminals. Such as Hex and his niece, Charmcaster.  
* As the series progresses, his cousin Gwen develops her own skills with magic. The sequel series downplays magic, tying it to alternate dimensions/energy aliens. But *Omniverse* brings most of it back. 

***3). Spider-Man:***   
^(TLDR: Spider-Man (a mutated human) fights energy vampires.) 

* Spider-Man (616a) got his powers from a radioactive spider bite. Turning him into a human "mutate" with spider-powers. 
* At the turn of the century, he is introduced to another spider-person, Ezekiel. Who got his powers magically. 
* Apparently, a special family of interdimensional energy vampires go universe-to-universe, draining life from "animal totems." The whole thing connects to the idea of "spider totems" and a magical connection between different superhumans.  
* Interestingly, the 616 Spider-Man are unique amongst animal totems. Because Peter got his powers from radiation and not just magic/super soldier serums, he is mildly "poisonous" to them.

***4). Invincible:***  
^(TLDR: Invincible (a half-alien superhero) fights dragons and such.) 

* The guide book implies that "magic" is just special subatomic programming, whose users lack the knowledge to fully understand it. But in-comic, it's just called magic. 
* Mark is half-alien, and his father's species is a classic flying-brick *Superman* archetype. 
* He encounters genuine magic, like an astral-projected dragon, an undead pharaoh, etc. 

***5). Dandadan:***  
^(TLDR: Possessed people, espers, and a Gundam vs. aliens, ghosts, and cryptids.) 

* Lots of different aliens exist. But ghosts/spirits also exist on Earth. This is apparently confusing to the aliens, who have never encountered ghosts on other planets. 
* Some characters have spiritual powers, some have ESP, and a few explicitly use alien tech. They fight other aliens, ghosts, spirits, cryptids, etc. 

***6). Versus:***  
^(TLDR: Wizards can't beat demons. So, they summon people from other dimensions. Unfortunately, this also brings killer robots, aliens, kaiju, genetically engineered humans, giant killer animals, curses, raiders, etc.)

* Like *Dandadan*, the cast is a mix of science-fiction and fantasy. 
* The main characters are from a sword-and-sorcery world. When they lose against the "demon king's army," they perform a spell that fuses their planet with a dozen-other dimensions. This brings them new technology to fight the demons, but also each universe's respective problem. 
* For example, they now have to deal with demons, giants, killer robots, aliens, kaiju, giant animals, etc. The wizards and super soldiers quickly realize none of the humans are capable of fighting their respective enemies. So instead, they work to trick each fight into fighting the others. 

[Fun trope]: Sci-fi characters with fantasy enemies.