When David tries to feed Ellie in the cage, she kicks the food tray away a few meters. However in some of the subsequent shots the food tray is right in front of the cage.
After she runs away from David and Ellie gets back to Joel, who is unconscious in the basement, with the antibiotics, about 15 minutes in, the blanket on Joel is pushed down. His right shoulder, part of his chest and his right arm down to his elbow are not covered by the blanket. The camera pans off of him and when it pans back the blanket is now straightened and pulled up so only his head is exposed but there was nobody moved the blanket.