Is a seed different from a nut?
There are two ways to define nuts, one botanical and the other culinary.

Botanical: It is a dry fruit containing one or two seeds, where the fruit does not open to release the seed. So, only indehiscent fruit are considered true nuts. eg. Walnut (image), pecans, chestnuts.

Culinary: A lot of seeds are called nuts even when they do not conform to the botanical definition. eg. Almonds, cashews(image).

Cocoa beans fall in neither category, so it is correct to say that the bag is nut free. Cocoa beans are harvested from a cocoa pod which is fruit like (image of cocoa pod with the seeds), so they definitely fall into the category of seeds and not nuts.

So the labelling on the bag is correct. As for the allergies, there may be people allergic to cocoa beans, but they wouldn't necessarily overlap with people who are allergic to nuts.