I'm a dual Peruvian-American citizen having taken my American friends to Peru I can attest that, while controversial, that the cheaper fares are meant to encourage Peruvian citizens who may not otherwise be able to afford air travel on their modest incomes.

This is along the lines of Florida resident discounts at Disney World etc. 

So to answer your question, the fine is per leg of the flight. You may be denied boarding of the flight all together. I know this is an old question but this can serve as future reference for anyone having this dilemma in the future.