When on Otto, the track visible is nowhere near the bucket, and there is no mine cart track near the bucket. However in the mines we see the bucket, and not only is King going in the wrong direction, but the bucket is not moving, when it should be.
When entering and exiting the music room, Sam shuts the door. However once inside the room, Sam goes through the door again, and when exiting the door is still open.
When going into Darkness' house, the pulley remains motionless. Even if we do not go anywhere else, just out, the elevator is on the ground and the basket is in the air, just like it was before Sam went in, and the pulley did not move.
A lot of the game's geography makes no sense; in particular, the geography of the Mines. The Mines connect to Darkness's tree house and we see tracks running in and out of it in multiple scenes. Yet the main entrance to the Mines is in a mountain, which does not connect to Darkness's house in any way. Furthermore, one scene in the "Upper Mines" has a door into Darkness's house, and another has that main entrance. We don't see any "outside" track in between those two scenes, even though there would have to be if the Mines have an entrance in a mountain and connect to Darkness's house at the same time.
Enter the "lower mines" (the area labeled "gold") and then, once you are at the big drop, go left. Sam and King will go through a tunnel with three overhead lights, then enter an area where you can either go down (into the gold vein) or up (to leave the mines and then come back in). If you go up and around the loops, Sam exits the cave through the left tunnel. We cut to a view outside the mines, and Sam exits through the left tunnel again, even though from that point of view, it should've been the right tunnel. Sam goes back in through the right tunnel, and then, back inside the cave, he comes in through the right tunnel. In other words, the shot of the loops outside the mines is flipped.
The wood in the track supports is dipped in lava, however it is very strong still. The heat in lava would have made any kind of wood go up in smoke.
The player can see what's underneath the geyser in the underground cavern. However, other than the crystals in the "geyser room," there is no evidence of the lava pools that surround the geyser above ground.
In the path with the flashlight in the mines, King can't make it to the top track with the flashlight on it unless he is able to pick up enough speed. This follows the laws of physics correctly, yet if he jumps without being held up by the winch, he goes straight down onto the lower track. The laws of motion dictate that he should have gone down in a parabolic motion (so similar to the way he moves if he is held up by the winch and makes it to the top track, but with less horizontal velocity so he falls before he makes it to the top track). The game shows him going ahead on the track and then straight down.
The lights are off at first in the flashlight room in the mines, and it is almost pitch black. However, it couldn't be pitch black because the lava would have illuminated the room.
Bug: If you go through the mines clockwise (that is, from the starting area into the 'gold' room, then into the room with the door into Darkness's house, eventually ending up by the washer and dryer), the "lava noises" continue once Sam enters the room with the washer and dryer, even though there is no lava present. The lava noises continue if you go into the abandoned mine shaft or back to the "starting room." They only go away if you go to a save/load screen or click the sock basket.
When Sam is rushing out of the "gold" area in the mines, we can hear him yell "whoa!" but his mouth is not moving.
The keys that spin around on the organ and the keys that are playing do not match the sounds coming out.
When the pipe organ plays music, he sounds like an electric organ.
How did the evil Customs trees get Sam's lunch box in an underground cavern, his flashlight in an abandoned mine tunnel or a river shack, or his mask into Darkness's house?