If you want to talk about two apples and an orange, you would not use fruits, but pieces of fruit.
John ate three pieces of fruit; he must have been hungry.
If you want to talk about different kinds of fruit, you use fruits:
John's three favorite fruits are apples, bananas, and papayas.
If you want to say John ate two orange segments and a quarter of an apple, you can say
John ate three fruit pieces
(not pieces of pieces of fruit).