Sheldon had not realized it was morning, and does not drink coffee, so where did the pot of coffee come from? Penny did not know Sheldon was still up so had not already come into the kitchen.
Just a thought, but even my low-tech coffee maker has the ability to start brewing coffee automatically at a predetermined time. In this case, however, even a non-coffee drinker would have been able to smell the brew which then begs to question why Sheldon would have to ask Penny, "Is it morning?"