Corrected entry: When Gromit is looking at the penguin's plan to steal the diamond, there are some pencils at the corner of the poster near where is says "Museum", but in the next shot, these pencils disappear.
Corrected entry: When Feathers shuts Wallace and Gromit in the closet we can see that there are several other items in there too. These disappear later when Gromit bursts out of it.
Correction: Gromit doesn't 'burst' out of the closet, Wallace does. Gromit falls out and the view of what's in there is still obstructed by Wallace. All that's in there are a few coat hangers anyway. They could easily have fallen to the floor considering what was going on.
Corrected entry: When the penguin comes to inspect the museum, all he brings is a pad of paper and pencil (we see this as he is walking by the café) but suddenly when Gromit spies on him he has a tape measurer with him. Just because this is a cartoon doesn't mean that the characters can pull things out of nowhere.
Correction: I believe this has already been corrected in relation to the gun that Feathers pulls out on Gromit. If a penguin were to be seen walking around the north of England with a tape measure and note pad, people would ask questions. As it is, its just an average, everyday penguin minding his own business. This is a normal occurrence in a world where dogs have opposable thumbs and a glove on the head is good enough to fool people into thinking you are a chicken.
Corrected entry: The penguin's eyesight ability keeps changing. At one point, he takes out a book called "Electronics for Dogs", and since he ends up switching the controls that are attached to the trousers onto switched to a remote, it's obvious that he can read the small print in the book. Also, when he comes to inspect the museum, he takes detailed measurements with a tape measurer. But when he stares at Gromit, who is hiding under the box, and Gromit blinks, he walks away without doing anything. And when Gromit is peeking at the penguin from under the covers and sees for the first time with the rubber glove on, the penguin doesn't see him.
Correction: The museum and the electronics book were at very close range. When Gromit is under the box and under the covers, he is a good few feet away. This makes all the difference to Feathers' eyesight. He is obviously near-sighted, a common affliction amongst plasticine criminal mastermind penguins who have human intelligence and the ability to disguise themselves as chickens with a strategically placed rubber glove.
Corrected entry: When Gromit looks at the calendar, he has a watch on his right arm. It disappears in later shots.
Correction: He takes it off. His birthday is coming up and he is giving Wallace a subtle hint that he would like a Rolex Oyster. Wouldn't you?
Corrected entry: When Gromit discovers the penguin's plan to steal the diamond, some of the pencils are scattered over the table. A little later, when the penguin brings Wallace back after stealing the diamond, the pencils are all in the jar.
Correction: Gromit is a very neat dog. Any dog capable of designing and helping to build and fly a rocket capable of reaching the moon and returning safely would have to be, of course. Prior to his nipping out to foil the dastardly plans of Feathers McGraw, a penguin who can reprogramme NASA designed equipment to accept a remote control, he sweeps up the pencils and puts them in their jar. This is a fairly obvious part of a film that is so fastidious in its depiction of reality.
Corrected entry: When Gromit is on the couch and then stands up you can see a fingerprint on his head.
Correction: After seeing the 'Making of' video which shows Nick Park and his crew wearing surgical rubber gloves while making 'Chicken Run', I went through the scene you mention scene frame by frame. No fingerprint.
Corrected entry: When Gromit leaves his house, he brings a comb, a bone, and an alarm clock with him. Yet before he comes back to the house, he is shown with a newspaper, a knife, and coins. None of these items are even included in Gromit's hut. So where did he get these things from?
Correction: The knife query has previously been corrected. As for the coins and the newspaper, simple: Gromit bought the newspaper with some loose change he had. This change was concealed about his person so as to be unseen by any potential thieves. This is common practice amongst dogs who can operate and repair electronic equipment, carry out complex engineering tasks, read and sort the morning mail and single-handedly foil the plans of International Criminal Masterminds.
Corrected entry: Wallace gets a leash and a collar for his birthday, Wallace puts the leash on Gromit, and then Gromit goes into another room, leaving the leash behind. Suddenly Wallace has it with him, and he attaches it to the techno-trousers.
Correction: Obviously you don't shop at the same place as Wallace. They have Two-For-One deals all the time, especially on fashion accessories for plasticene dogs who can ride motorcycles and solve complex calculus problems. Obviously Wallace bought two of the leashes in question.
Corrected entry: When the penguin first arrives at Wallace and Gromit's house, he has a brown suitcase with him. When the penguin is sitting on the bed, the unopened suitcase is a different color.
Correction: The lighting changed, meaning the colour seems subtly different. They used the same prop throughout, and there is no film mistake.
Corrected entry: During the train scene at the end, the penguin fires three shots at Gromit, and each time it leaves a mark on his helmet. But suddenly there is a shot of Gromit and his helmet only has two marks.
Correction: There are only two marks VISIBLE. The helmet - a glass lampshade - spins on Gromit's head when the bullets hit it, so the bullet mark on the other side isn't visible in this shot.
Corrected entry: There is more jam on Gromit's head than there is flung from the jar.
Correction: No, there isn't. It spreads out when it hits his face, so it looks like there is more.
Corrected entry: When Gromit is having breakfast at the beginning, there is no red button on the table. Then when Wallace asks for jam on his toast, there is one that Gromit hits. Later we see the whole table and the button is gone.
Correction: It fits into a recess on the table and pops up when you need it so it won't get in the way. Would you like a permanent fixture on a flat table?
Corrected entry: When Wallace looks at all his bills, there are two salt shakers on the table. After Wallace goes to get his piggy bank and comes back to the table, they are positioned differently from before.
Correction: No, the camera angle is different and the salt cellars are in the forefront of the scene, so they appear to have moved.
Corrected entry: When the bread pops out of the toaster, the center of the toast is very black. Then when Gromit has it, we see that it is nice and brown, even though we should have been able to see the black parts.
Correction: This is the North of England, chuck. We scrape burned toast here. Obviously that is what Wallace did, but why show that in a film?
Corrected entry: During the train scene, Gromit is dangling from a lamp on the ceiling. Then Feathers McGraw shoots the lamp, Gromit falls onto the train, and the lamp is on his head. But as earlier seen, there is a light bulb in the lamp, so shouldn't we have seen and heard breaking glass?
Correction: The bulb didn't break, obviously. It dropped to the carpet and bounced or rolled away, plasticene lightbulbs being as robust as they are.
Corrected entry: When the penguin tries to rob the diamond, he uses a mechanical arm from inside Wallace's helmet to grab the diamond. However, the arm is not very precise, and Wallace needs to be exactly over the diamond to get it. When the diamond falls from the mechanical arm, it falls slightly to the right of the arm, but the arm is able to grab it. This is not possible. The penguin did not move Wallace to get it, and even if he had, this would have taken a few seconds, by which time the diamond would have definitely struck the floor.
Correction: Obviously you are unfamiliar with the exact capabilities of the 'telescopic-arm-mounted-remote-controlled-robotic-claw-which-can-fit-inside-a-two-inch-thin-helmet' (TM). Whenever it drops something, it has the ability to calculate the trajectory along which the dropped object travelled, then having correctly aligned itself thus, retrieve the object at a point relevant to the speed of its travel. This safety feature is unique among helmets manufactured to fit the needs of criminal penguins, and is undoubtedly why Feathers McGraw chose this brand of helmet above others.
Corrected entry: Wallace cuts out a piece of the box so he can spy on Feathers McGraw. When McGraw walks away later, the piece of the box is gone.
Correction: They are in the north of England, and the winds are ferocious up there. It blew away.
Corrected entry: When Wallace comes to spy on Feathers McGraw, his paws are empty. But then when he is under the box, he has a swiss army knife with him.
Correction: Wallace doesn't have paws, he has hands. Gromit is an unusual dog - he can read, ride a motorcycle, steer a rocket to the moon, make tea, bungee jump, count money, work out complex electronic designs. A dog like that can do anything, including secreting pocket knives about his person(?). Maybe he hid it in his huge collar?
Corrected entry: The penguin's hand is empty when he bumps into Gromit after shutting Wallace in the closet, then he suddenly pulls out a gun out of nowhere.
Correction: Feathers McGraw is an International Criminal Mastermind. He has obviously had a special holster made to hold the gun in the small of his back so he can appear to pull it out of nowhere and terrify his opponents. This is a perfectly common phenomenon in a world inhabited by dogs with advanced engineering skills, remotely controlled trousers than can walk up walls and...you get the picture.
Correction: The 'next shot' is a close up of the plan, and after that there is a close up of Gromit. He lets go of the plan which rolls up by itself, and who knows where the pencils could have gone? They probably fell on the floor.