When Penny sneaks into Sheldon's bedroom in the middle of the night to ask him a question about her video game, she leaves the door open slightly. She talks to Sheldon for a few minutes, then the scene changes to Leonard hearing the end of their conversion through the door. When the scene changes, the door is clearly closed, and Penny nor Sheldon would not have had any time to close the door.
Among the groceries Penny drops on the floor is a purple bag that falls on the floor, disappears, and then reappears between shots.
When the guys restart the music that makes the cornstarch and water "dance," the music plays a few beats before the substance starts to move.