Clarks asks how deep did they drill before closing the well and the foreman states about six miles and Lois exclaims, that is almost to the center of the earth. How a reporter could be so wrong on her facts is surprising. Six miles is about 0.15 % of the actual distance.
When one of the mole men gets shot, he falls on the other side of the upper dam, but Superman catches him as he falls on the front side of the dam.
As Superman walks down the porch steps toward the angry mob, he says, "Put the gun down, Benson." No one notices that Superman shouldn't know Benson's name; it was Clark who met him.
When Lois and Clark drive up to the well to look around their car lights are on indicating it is night yet it seems to be dusk at best. Even when they exit the car they cast distinct shadows. All the while the whole town gathers looking for them it appears to be day or again at best dusk. The only difference is when Lois or the little girl see the little men in the window it looks pitch black outside. Also when they are on top of the dam it appears to be night time too.
When the little men are exploring by the flower bush they are walking on grass but then they get scared when they see a snake slither by but the snake is on dry dusty ground with no grass.
When the townspeople gather, Clark warns them that the "creatures" may be dangerous, but he never mentions that are likely radioactive.
The little men exit from a capped-off well however they shouldn't be able to unlock it from the inside. The locks just pop open as if by magic.