Jacob's right hand when Sally is throwing the blocks against the mirrored window.
When Sally approaches the tower, she is shown standing still, yet a long shot shows her walking.
When Sally and Jake are sitting at the table with the blocks, Jake picks up an orange one and put back a yellow one.
Kathleen Turner's character says that all railways in the world have the same gauge which is absolutely not true. Examples: Spain - 5' 6"; Ireland - 5' 3" and 3'; India - 5' 6", 2'6" + 1m; Peru - 3'; Portugal - 5' 5 9/16" (1.1665m) + 1 m; Russia - 5'; East Africa - 1m; Nigeria - 3'6"; Sierra Leone - 2'6"; South Africa - 3'6"; Burma - 1m; Ceylon 5'6" + 2'6".
In the 'tower in the woods' scene, the full moon is shown vertically above: this only happens near the equator (i.e. in the Tropics), but the scene is in the USA.
When Ruth Matthews is reading prime numbers out of a book to two children, one of the primes is 3041527. But 3041527 is not a prime. It is the product of 1741 and 1747.
In the viewing room scenes, the room from which the viewing is done is as brightly lit as the viewed room: for the 'one way mirror' to work the former must be dimmer than the latter (in fact usually it is virtually unlit except for desk lamps for making notes).
When Ruth scans in the pictures of Sally's house of cards to the computer, the photos are black and white, but in the virtual reality model, they are color.