Short list...
Sometimes it makes no sense.
There is no ham in hamburger.
Neither is there any apple nor pine in pineapple.
If teachers taught, why didn’t preachers praught?
If a vegetarian eats vegetables, what does a humanitarian eat?
“Overlook” and “oversee” have opposite meanings, while “look” and “see” mean the same thing.

Exceptions to rules.
Word order.
Pronunciation.
Emphasis.
Homophones.
Synonyms aren't necessarily interchangeable.
Idioms.
Etc.