Be Careful What You Wish For: Because you are going to get it. Yay! Lots of perfectly OK wishes went sour because of literal interpretations. Some wishes were just silly and their consequences proved lethal.
Becoming the Genie: Jenn's third wish was to have great power and a long life... The original genie turned her into one as well.
Black Comedy: The death of the two Stokes brothers is portrayed as funny. One of them finally comes up with a good and clever wish — a new pair of legs at that moment. Precisely at that moment their home blows up, and the legs land next to Mulder and Scully who are coming to question them.
Blah Blah Blah: [Jenn reading a draft of Mulder's wish] "'Whereas, I have one wish left and desire to use it most effectively for the good of all mankind...' Yada, yada, yada. "'Here on this plane of existence...'" Hmm... Hmm-hmm. What, are you a lawyer?"
Blessed with Suck: Turns out invisibility is not that cool because other people might not see you when you are crossing a road and they are driving a truck. Dun-dun-DUUUN.
Came Back Wrong: One of the Stokes brother wishes to be invisible and gets killed by a car when trying to cross the street. When his brother wishes for him to come back alive, he appears as a shivering necrotic corpse, unable to speak. His brother wishes for him to be able to talk in spite of the genie's warning, and he screams for minutes straight. After he's all screamed out, he attempts to light the stove to warm himself, complaining he "can't feel his blood." He fumbles the matches with the gas on full blast for many minutes, and when he finally does light one, the trailer explodes, killing both brothers permanently and ejecting the genie.
Deader Than Disco: In-universe. Jenn claims people want her to make them cool like the Fonz or whoever is the big name now. Mulder snarks that she has been out of circulation for a long time.
Eye Scream: Discussed by Mulder in order to defy it. The idea of eyes growing on stalks is squicky enough.
Mulder: I have to be [a lawyer] with you. (...) I'm not going to leave you any loopholes. I'm not going to let you interpret this as an edict to bring back the Third Reich or to make everyone's eyes grow on stalks.
Facepalm: Scully is embarrassed that she invited some scientists from Harvard to see a proof of paranormal which unfortunately disappeared. She facepalms with both her hands.
Invisibility: The last wish of the first Stokes brother. Jenn sees the potential for being perverse and how stupid this wish actually is.
The Last Man Heard A Knock: Mulder's first wish was to have "peace on Earth", only to find himself the only person left on a vacant planet. Fortunately, while there weren't any other humans, the genie was still around to hear him revoke his wish.
Literal Genie: Jenn interprets the wishes she must grant very literally. For instance, when one guy wished his boss would shut up, his lips were sealed together and his mouth basically disappeared from his face.
Our Zombies Are Different: What Anson essentially comes back as, though he doesn't try to eat anyone's brain. He can't even talk until Jenn makes it possible, whereupon he immediately vents his unhappiness re his situation.
The original genie — Jenn wished to have power and a long life, and so he made her a genie, too.
Jenn was very mean but interpretation might differ whether she fits this trope. She did try to suggest that the crippled Stokes have his legs restored, but they're too thick to get the point until it's too late.
Rhetorical Request Blunder: Anson Stokes' first wish. He didn't know he had found a wish-granting genie yet. He wanted his boss to shut up.
Happy Days: Jenn claims a wish is often something like "make me cool like The Fonz" or whoever's the big name now.
Three Wishes: Jenn the genie grants three wishes to whomever finds her.
Too Dumb to Live: The Stokes brothers. One of them lost his legs in a car accident when they were smashing stuff with a baseball bat while driving in a car. They simply cannot come up with normal wishes and they are not Genre Savvy enough to word carefully their wish to reverse the mess their original wish caused. They really had it coming.
Wasteful Wishing: Anson Stokes' first wish was that his boss would shut the hell up. He did. Poor guy, his mouth got literally shut up. His second wish is a yacht, which gets plonked right next to his trailer with no means of moving it to the ocean.
World of Silence: When Mulder wished for world peace from Jenn, every human in the world except him vanished, thus granting his wish through this trope. Mulder runs out of his office and sees deserted buildings and streets with only empty cars and buses.