When the church is viewed from the outside, the main door is a Norman arch (semi-circular). From inside, it's a Gothic (pointed) arch. It's the same door - Victor boots it open from outside so you can clearly see there is no church porch.
After Wallace and Gromit capture the rabbit in the beginning, a banner for the vegetable competition shows that there are four days left. The next night, after Wallace tries to brainwash the rabbits, the calendar where Gromit has marked the days until the competition shows that there are five days left, before Gromit crosses off one more day, making it four.
During the breakfast scene at the start of the movie, there is some salt and pepper on the table. In the early shots of that scene the salt and Pepper are farther away from Wallace, but when he pushes the pepper it is closer to him.
When Wallace and Gromit are trapped by Victor's dead end tree in the road, Victor throws the hatchet into the tree next to Wallace. Wallce, nor his clothes, are touching it. Yet when Wallace tries to run off, we see his suspenders caught in the hatchet. The very next scene, Wallace is next to the tree again, and again his clothes are still not caught under the hatchet.
During the town meeting scene. Lady Tottington is in front of the bible with angel wings and a light above her. But in the shot after it cuts to Victor, the light is now not above the bible with wings.
There's a full moon for at least four nights in a row.
Just before the title of the film appears we see the full moon above the rooftops. The moon is on the left of the scene, but the shadows of the chimney stacks are also to the left. They should be to the right.
There's a full moon for four nights in a row. A full moon can only occur once (or twice for a blue moon) a month.
The rabbits in the film have pig-like noses, while real rabbits have small triangular noses. Real rabbits don't have paw pads either.
During the airplane chase sequence, one of the electrically operated planes crashes. It presumably carries no fuel on board, and yet it explodes in a massive fireball.
The prices in the fairground scene at the Giant Vegetable Contest are in the old pounds, shillings and pence, showing that this film is set before this form of currency was abolished on 15 February 1971 (indeed, Gromit's calendar in one scene shows that 1 September is a Thursday, so the latest this film could be set is 1966). Yet Pesto's technology uses LEDs, which didn't become available until the mid-70s, and diode lasers, which weren't available to the general public until about 2000. However, Wallace has been shown to be a genius inventor, it's quite possible he invented all of these things himself, long before the items became available to the public.
You can see the thin metal pole they use for stop motion on Gromits front right foot.
The hammer on Quatermaine's flintlock doesn't have a flint, but it makes a spark anyway.
When Gromit builds Hutch"s heavy-duty hutch, the door opens outwards, yet he puts a wood block for a lock on the outside where it would do nothing.
During the town meeting. If you listen closely to the man and woman behind Wallace, you can hear that their voices where swapped.
It's unknown how the Were-Rabbit when having turned back into Wallace always ends up back in bed by each morning with pajamas after going round town each night eating everyone's vegetables.
Surely the residents would know that the Were-Rabbit would be a human, back to normal when the sun rises, hence the name "Were-Rabbit", much like a Werewolf. Not even the Vicar knew this.
Despite all the incidents caused by the Were-Rabbit, all the incidents it caused seem to be back in good condition each morning. Same said for what's been happening to the Pesto Van throughout the film (like after it had been following the Were-Rabbit underground on the 2nd Night).
The business model of Anti-Pesto is unsustainable (except if they received government subsidies or it was a Ponzi scheme.) Keeping the rabbits alive and even feeding them carrots instead of cheaper biomatter would have to lead straight to bankruptcy. Customers would have to pay them a lot more than their harvests are even worth to keep that up.
When Wallace comes down for breakfast and reads The Morning Post, the paper's subtitle reads "The paper with it's finger on the pulses". This should read "The paper with its finger on the pulses". "it's" means "it is".
When Wallace and Gromit capture the rabbit at the beginning, it is briefly subdued when Mrs Mulch's husband's teeth come shooting out of his mouth and hit it in the face. But as the rabbit is being taken away it grins, revealing the teeth in its mouth, and Mrs Mulch is heard shouting "Reg! Me teeth!", even though they were clearly his teeth.