Accidentaly, I ate chocolate chips that were chametz during Pessach; it was not negligence because I bought it from the kosher for Pessach section of the supermarket and till the last moment, I thought it was chametz free. Should I do anything to compensate this accidental averah?

Chocolate chips are not Chametz, they may not be made special for Pesach and therefore should not eaten on Pesach, but are definitely not Chametz. Your Teshuvah should be in future to make sure whatever you buy is truly kosher for Pesach even if it is in the Pesach aisle.