The gift box on the left of the screen was a new feature added by the devs during the last maintenance as a level up reward for reaching level 30. For those who had already hit this milestone the rewards were already available.
You can hold as many heroes as your research will let you up to a maximum of 12. There is no limit as to how many of each colour hero you can have. Hero cards are different, since you don't own the hero until you use the card. With hero cards you can own as many as your bag space will allow. If your bag was full at the time the game will not have let you collect the rewards, so unlike with dungeon drops, you cannot lose a hero card from areward due to a full bag.
Did you notice if you gained 1million copper soon after getting the cards? Which card were you missing? It maybe that you accidently 'sold' one card for copper, therefore only allowing you to actually use one that remained.
If you are still uncertain then I would suggest sending in a ticket to game support, and explaining your issue. The support team can review your account to see what happened to the card. Unfortunately, if you did accidently copper the card it is unlikely that they will be able to return it to you.