After cocoa beans are harvested they need to be fermented. This means that they are put in an earthen pit near where they are harvested and covered with leaves. In the hot sun they ferment (rot) and then can be shoveled out as mature cocoa beans. Of course during this process lots of insects are present.

Almost all chocolate have bugs in it, because it is too expensive to manufacture without bugs. The FDA allows a certain amount of bugs or animal in most foods you eat. Almost all manufactured food you eat comes with an animal you won't think would be in it.

Cottage cheese is allowed to have 10 fecal coliforms / gram (fecal coliform being bacteria like Escherichia coli that is normally associated with human and animal feces). Doesn't mean that it will hurt you either.