(at around 1h 3 mins) When Kirsty opens the box while in the hospital, the walls begin to part and you see tons of cobwebs being stretched between the two walls. In the next shot, Kirsty is shown walking toward the opening but the cobwebs are gone.
(at around 55 mins) Julia's third victim has a (dubbed) American accent when he enters the house. When he is pleading with Julia to save him from Frank, however, he speaks in a British accent.
When seen from inside, the attic has a single window made from four separate panels of glass. However, from the exterior shots, the real house has six panels. It makes obvious that the internal scenes were shot elsewhere: in fact, they were the only scenes filmed in a sound stage.
(at around 1h 1 min) When Kirsty first wakes up in the hospital bed, the tray-table in front of her is empty. The doctor comes in and deposits the puzzle box on the table. He says he'll get her a phone after they've talked. However, directly after he leaves, we see that a phone has appeared on the table. It is neither mentioned nor used.
(at around 58 mins) When Kirsty discovers Frank he delivers his catch phrase "Come to Daddy." Later, when Kirsty is fleeing the house with the puzzle box the line is heard again but it is in Larry's voice even though Frank hasn't replaced him yet.
(at around 5 mins) When Pinhead pieces together the remains of Frank's face, the eyes are seen attached to the facial skin (anatomical error). If chains were tearing the skin of his face off, his eyes wouldn't come with it (unless they were hooked as well, which they weren't).
(at around 1h) Nuns would not just walk past a woman with blood on her shirt looking like she's just been attacked. They would have helped her immediately.
Despite having been revealed to be Frank wearing Larry's skin, Frank continues to use Larry's voice, even when in pain.
(at around 1h 5 mins) When The Monster in the tunnel chases Kirsty back towards the hospital room, you can see the trolley and wheels the monster is being wheeled on. Also whilst Kirsty is running away, the camera cuts to the tunnel, and it seems she is running the wrong way (the tunnel with the painted disappearing point appears supposedly ahead of her).
(at around 1h 6 mins) When Kirsty is trying to get out of the hospital room she says the door is locked. However, when she walks away from it we can see a push-plate on the door and no handle or lock mechanism.
At 27:18, an Intercity 125 train with a British Rail logo passes, contradicting the film's American setting.
(at around 1h 4 mins) When the Engineer chases Kirsty, the trolley and crew pushing it are visible.
(at around 1h 18 mins) When Kirsty bumps into the corpse and the maggots fall out,that would suggest that the decomposing dead man had been there for some time. Even if it was well hidden by Julia (and perhaps also by Frank) the smell of a decaying body or two would be noticed.
The house was in no condition to be moved into, in less than a week. It needed major renovations and clean up before it was inhabitable.
(at around 1h 19 mins) When Kirsty is at the top of the stairs hiding from Frank, a shadow of the boom mic is visible on the top corner.