There is basically no way to tell this in advance, because the travel agency has no incentive to provide you with this information. The only thing you can do is see if the fare is bookable on delta.com for the same price - if it is, it is probably a normal fare. However, this is not always foolproof.

In this situation, the travel agency screwed you. However, in the future if you view the receipts on delta.com within 24 hours you may be able to tell if it is an unpublished/discounted fare and try to get a refund.