Yup. It's unfortunate, but happens from time to time.
Remember, that the order in which you play your cards is important, as different abilities can be triggered/maximized depending on the order in which they are played.
I've found that the above scenario you presented can sometimes be mitigated if you play the cards in your hand in a particular order and are able to avoid shuffling your discard pile into your draw pile until later in the turn.
Also you can luck out the other way around. Some Dark Arts effects and villains make you reveal the top card of you deck. If you don't currently have a deck, then awesome.