Some people cannot tolerate citrus (or things with citric acid added).

Some fruits have acids that stimulate the GI tract. For example people with hereditary angioedema cannot eat fruit because this acid releases bradykinin in the GI tract and causes GI upset.

Some fruits like bananas and pineapple have serotonin in them and this may cause looseness.

I just can't handle fruit. Sometimes I have a little, but very little and only once a week or so.

There is one thing about elimination diets. I've read that if you do them, avoiding a certain substance for a while (usually longer than 2 weeks) you may be able to each a bit of the trigger food once a week or so (but not daily or often). The intolerance sort of fades, and then takes a while to build up after a long abstinence.

MSG can cause many nerve symptoms and increased pain.
(monosodium glutamate).

The congeners in wine and beer and some liquors can cause problems too.

Grapefruit and its juice can cause many RX drug reactions, and the list of drugs gets longer every day. This is the result of inactivation of the Cytochrome enzymes in the GI lining, allowing more of a drug to be absorbed.

Nightshade veggies especially can cause burning pain all over, and/or in the feet. Sometimes there is a slight delay of this into the next day. The culprit is the alkaloid solanine found in the veggies.

There are also histamine releaser foods and histamine containing foods. There is a thread in the Subforum about this.
Histamine released suddenly affects the skin, and flushing, rash or sweating may occur with it.
http://neurotalk.psychcentral.com/thread161714.html

Each person will have their own combination of intolerances if they are present, based on their lifestyle and history.