In Italian "-one" suffix makes the noun as "big one" and "-ino" makes it "small one"; What about those words that basically has suffixes "-one" or "-ino" by their own such as torrone? Is there any exception that doesn't follow this rule?
There are no “exceptions” because there is no “rule”.
And the “rule” not being such works both ways: there are many words you can't affix -one to to mean a big specimen, unless jocularly (pane is “bread”, but no one would say seriously panone); and there are many, many words that end in -one without implying that there is the big version of something, but just happen to end in -one, like the above mentioned torrone, and mattone, bottone, furgone, montone, ottone, canzone, procione, regione, cotone and lots more.
Moreover, there are words in -one that are related to another one, but have taken a different, specific meaning: for instance a cassetto is a drawer, but a cassettone is a chest of drawers, not a big drawer; similarly with calza and calzone, carta e cartone, santo and santone, neutro and neutrone and so on. Or subtler cases where the meaning of “big” remains, but the words are nonetheless used only in some contexts, not as a generic big item of that kind: a guantone is used only for boxing or baseball, not for a generic big guanto (glove), and analogously for tromba and trombone, tenda e tendone...
All of the above, of course, also apply to -ino.
In addition to what @DaG said (there are no rules), there are some ways to make an accrescitivo or diminutivo of words that happen to end with -one or -ino.
One technique is to use the alternative suffixes -cione and -cino. In the case of torrone, the smaller version of if would be torroncino. Jokingly, one could also construct words like torroncinone (a big small torrone).
In other cases, to make a diminutive of a word that ends in -ino, one can change the suffix to -etto or -uccio. A small or young bambino (that is already small or young by definition), would be a bambinetto, for example. However, being the diminutive of something that is already small, words like these usually carry some additional context-dependant meaning.
In yet other cases, you just cannot use a suffix. For example, from the word passione you could construct passioncina, but a word like *passionona would sound too weird (at least to my ears).