There are generally three types of encounter / player obstacle.
Conscious Physical: involving humanoids, robots, animals, aliens etc
Environmental: storms, solar flares, volcanoes, mechanical failure etc
Anomalies: these are the sort of encounters you get a lot in shows like Star Trek, another example would be 2001 Space Odyssey. In these encounters an away team has to figure out what the anomaly is before figuring out how to deal with it.
5th Dimension Handwavium
In my Traveller handwavium what we percieve as gravity is only the 4D representaion of a 5D phenomenon and both the Jump and Manouver drive work by manipulating these forces.
Psionic talents like teleportation follow the same logic, except instinctively i.e. Jump is a kind of teleportation.
The Cthulhu Mythos is integrated into the universe in the same way.
This background handwavium can provide the rationale for a lot of anomaly type encounters so exploration type campaigns aren’t all bug hunts.
As gravity is required for both Jump and Manouver drives this allows for gravitational navigation hazards: the equivalent of storms, whirl pools, rip tides, turbulence etc.
Part of scout service initial exploration is finding this sort of anomaly and marking them. They mostly can’t be fixed, just marked as a hazard (but some can e.g. enter a tesseract in space, press some buttons and its gone).
Anomalies also exist on planets – places where the 5D is intruding onto the 4D universe.
Example: Space Ghosts
Some site is registered as an anomaly on a scout survey and an away team is sent to investigate. It could be a cave or an abandoned base or orbital station.
The ghosts are dreaming 5D creatures who display as slow moving white translucent humanoid figures. They are sentient but dreaming so can’t be rationally communicated with. Telepathy indicates dreaming. They are not intentionally hostile but curious – they move to contact the players and reach out to touch with their hands. Hands unnaturally cold: produce frost bite on exposed flesh, make any equipment brittle so it cracks and falls apart. They will follow players (slowly) but won’t cross the site threshold.
Space ghosts are immune to physical damage but sensitive to emotional projection: anger, hate, rage – once figured out firing a weapon with rage and anger can wake the 5D creature up and the ghost disappears; burst fire adds a DM, autofire adds more (ammo might be a problem).
With this 5D handwavium any supernatural monster from any game can be used as an anomaly encounter as well as Cthulhu creatures.