Dye packs are small devices that explode after being armed and placed in the container the money is stuffed into. When the dye pack is armed and later explodes, it marks the money, making it easier to spot and identify if the crook is caught. The other effect is that it permanently makes the money, or a significant portion of it, useless.
Bills on the bottom of the stacks in a drawer can be marked to make them easier to ID later. Foley knows that and so he orders Loretta to avoid giving him any marked bills.