This may not be considered “canon”, as it’s a passage from a 1990s-era New Adventure novel. But at one point, the Doctor & companions (Ace and Bernice) travel back to Swinging London in the mid-60s and the Doctor drops a whopper dose of acid (four tabs.) He points out to his companions that LSD would not affect his non-human physiology the same way it would for them and goes on to mention that one single aspirin would kill him faster than cyanide would a human.
I forget which NA novel it was, but someone else must remember this. It was actually kind of a big deal in England when the novel was published – geeks were in an uproar about the Doctor getting psychedelized.
There were some pretty heavy religious tones in that movie. I’m pretty sure that the glasses were full of holy water.
Other things related to the topic:
In Babylon 5, Minbari get homicidal when they drink alcohol.
Also in Babylon 5, there’s a mention that Centauri can’t digest human junk food. They eat it anyway, since it tastes so good, but then they throw up.
In 2061 (by Arthur C Clarke), the alien that eats the research team dies horrifically (if I recall correctly) because of the biochemical differences.
In one of the Honor Harrington books, there are mosquito-analogues that like to bite humans, but die because the blood they take is poisonous to them.
And, finally, one of my favorite books is Sector General (by James White), which details the culinary adventures of a chef who has to prepare the foods of all the various species at an intergalactic hospital.
Kzinti are repulsed by the idea of eating plant matter; the mere thought of it makes them physically ill (though this seems to be a cultural issue more than a physiological one).
Per Andy L, Kzinti also seem to have the notion that because humans eat disgusting plant matter, that’s all that we eat. There’s a scene in one of the stories where a Kzin who has captured a human attempts to be polite by offering the human a salad, rather than the perfectly-acceptable steak the Kzin himself is eating.
And back to the OP, it’s highly unlikely that aliens would have any reaction to spicy peppers (or at least, not anything like the same reaction that we have). That’s not even universal to Earthling life, but restricted only to mammals: Birds completely ignore capsaicin, as do reptiles, fish, etc.
Though the Kzin don’t cook their steaks (they serve them warm but uncooked), and find the smell of cooked meat about as appealing as we find the smell of burnt hair or burnt rubber. If you don’t want your steak raw, the polite thing would be to take the salad.
Kurn, Worf’s brother, tried some human food just to be polite (for a certain definition of the word “polite”). “I will try some of your burned, replicated bird meat!”
Read the John Wyndham novel that the film is nominally based on (although they heavily dumbed it down) The Triffids, it’s likely, were sentient, although not alien.
The BBC made a faithful adaptation of the novel that’s pretty good. Then they went and made an incredibly unfaithful one, to make up for it.
In Doctor Who the Raxacoricofallapatorians are killed by acetic acid, so vinegar, pickles, certain soft drinks, ketchup, sweet and sour sauces, various salad dressings, and a lot of other human foods would be deadly to them.
Also, Raxacoricofallapatorians are about 8 feet tall with claws and sharp pointy teeth so yeah, scary looking. Some criminal elements among them also disguise themselves by wearing actual human skins so that’s pretty scary, too.
An example which doesn’t quite fit the OP is the story “Gateway to Elsewhere”, by Murray Leinster. It’s set in an Arabian Nights-like land where the humans are at war with the djinns. The djinns’ main weakness is that they’re all, every last one of them, violently allergic to ragweed, where “violently” is used in the Hiroshima-and-Nagasaki sense of the word. They’re not quite aliens, and it’s not food, but it is an example of a substance which is only mildly annoying to humans being lethal to the scary and more powerful nonhumans.
IIRC chocolate either gave them tremors or caused cardiac arrest.
I don’t think they could digest any cooked food. They had a definite preference for organ meat as opposed to the muscle tissue humans prefer. Cathy was a vegetarian. Also she made that lasagna with marshmallows so her lasagna might have made humans sick too.