Differentiating Science Fantasy

Often science fantasy as operationalizes in rpgs is just some flavor of rpg fantasy with ray guns or robots, or "ancient technology" as the default explanation for something strange. (In fact, high tech "science" often  becomes the extraordinary thing in a setting full of magic but completely conventional in its portrayal of magic.) There isn't anything wrong with that, but science fantasy fiction points the way to making the genre feel different from a fantasy setting that just also has some lost tech.

More Psychic than Spellcraft

The magical effects (when they aren't technology mimicking magic) often tend to resemble psychic powers instead of spells or rituals.

Non-Medieval Society

In C.S. Friedman Coldfire series, the owners of a bookshop who are the victim of an attack by the magical agents of a dark lord of sorts have to worry the authorities will think they committed insurance fraud. There's no reason a science fantasy setting has to limit itself to mixing science fiction and the (pseudo-)Medieval. Elements of any era could be fair game, depending on the setting.

Device Dependent

In science fantasy, more magical effects are going to be the use of a device or chemical rather than a spell. A Polymorph effect, for instance, can still exist, but it would be from a transformation machine or "atavism ray" or the like. A variant on this is when a classical magic item turns out to be a technological device, like when Travis Morgan's putting a bullet into Deimos' crystal ball and we see circuitry inside.

Subtle Reminders 

Little details that point to the nature of the setting often help set the mood. Post-apocalypses (fantasy and otherwise) tend to excel at this. King's Dark Tower stories have a witch writing a note on an old Citgo receipt pad, for instance, but having an old device put to a new purpose is a device that works in science fantasy too.

Consistency

While in many situations "science vs. magic" in a fantastic context would just be cosmetic, it's important to keep in mind the different origins and make sure the details match. For instance, orcs that are embodied spirits of evil ought to operate differently in any number of ways compared to orcs who are a transplanted, anthrophagous alien species or orcs that are bioengineered servitors.