Since they haven’t been mentioned yet: the designs of Elgyem and Beheeyem are based on aliens:
Unfortunately their cards aren’t too alien-oriented. Although I guess this could be a ‘spaceship’. 
Some other Pokémon that come to mind, besides Deoxys and Gigantamax Orbeetle that have already named:
Magnezone:
Genesect:
With some fantasy you could say this Minior in outer space just crashed out off or into a space ship. 
This Clefairy / Hypno pair usually gives me abduction vibes:
Some other things that come to mind:
- Skyridge has a bunch of cards with crop circles (or I should say Pokémon-shaped figures): Skyridge Story Artwork
- Some other space-related Pokémon (although nothing really with aliens / UFO): Cleffa, Clefairy, Clefable, Lunatone, Solrock, Deoxys, Minior, all the Ultra Beast Pokémon, Cosmog, Cosmoem, Giratina, Dialga, Palkia, Poipole, Naganadel, Jirachi, etc.
If we include non-TCG Pokémon cards as well, this one would be perfect:
And these come to mind as well:
Greetz,
Quuador