When John tells Penny she can't stay at the drill site, closeups have her hair neatly combed behind her left ear, while in the long shots it flows over the top.
Penny goes to see Mr. Nobody, and she is carrying a book. The viewer sees the book in her hand. Penny has the book in her hand when taking a drink from the river. The next shot shows her walking to the cave where Mr. Nobody lives, but she is no longer holding the book. Then the next shot shows her holding the book once again.
When Will throws Penny's "quartz rocks" into the air, they land on the chessboard, on which Dr. Smith and the Robot have been playing. The opposing king pieces, however, are adjacent to one another. This would be impossible since a king piece cannot be moved into a checkmate position. Even more egregious, shortly thereafter, Dr. Smith tells the Robot he was on the verge of checkmating it.
After Don and Dr. Smith detonate explosives, parts of the cave collapse. For several seconds after the explosion, one of the stalactites sways back and forth.
As Doctor Smith walks across a sandy area, you can clearly see that the sections that make up the background don't match and you can see the seams in it.