We say "one" when talking about the number of apples. In a situation where we might say "two apples" or "three apples", we say "one apple". It is the normal answer to a question like "how many apples?".
In most other situations, we use "a/an/the" before any countable noun such as apples. So "a/an" is used much more often than "one".
Do you have anything to eat? Yes, I have an apple.
If you are hungry, I have an apple you can eat.
I knew this meeting would last long, so I brought an apple.