Plot hole: The alien digs an extensive underground network of tunnels beneath the cemetery without leaving huge piles of dirt above ground. (01:29:05)
Suggested correction: There appears to be a large pile of dirt between the building and road [@ 00:54:31] when Joe went to the cemetery to "visit" his mother. Perhaps there is more behind the building. Or, based on how far the creature could toss large appliances, the "monster" might have flung some of the dirt far away (to the next county?).
Continuity mistake: After the train crash and Joe is back home, his dad wakes him up and he is facing off to the side as he opens his eyes and starts to lift his head. It cuts to a different angle showing the white cube in the foreground and suddenly Joe is looking up fully at his dad. (00:26:40)
Suggested correction: I watched a few times and saw a rather good, smooth series of movements - they did not look awkward at all. I did not see what you saw, which leads me to suspect corrections were made or your DVD player "skipped."
Maybe one more person will check his/her copy.
A small hiccup in the stream might be an even better explanation for the discrepancy - in which case "I saw what you didn't see" would be more accurate than "I didn't see what you saw."
Audio problem: The train horn sound changes from what it was to a different horn sound when it passes the Lillian Depot. Then it changes back. (00:16:30)