At some point, a character says, "And cut." You don't "cut" a live TV broadcast. You say, "We're out" or simply "out." (The same kind of goof is noticeable in _Monsters vs. Aliens (2009)_.)
In the beginning scene, where Penny and Bolt are acting out the chase scene on the playback monitor, the producers are enraged over a boom mic showing up in the shot. Yet seconds earlier during the actual scene, you don't see the boom mic in the upper right corner.
During his cross-country adventures, Bolt's signature lightning bolt mark on his side fades away, returns and then fades again.
The front of the train is visible going under the bridge just before Bolt, Rhino, and Mittens jump. Later, both ends of the train are visible. The train is much shorter than the length of the time between the first sighting of it and them jumping would suggest.
During the scooter chase, Penny and Bolt pass through an intersection pursued by 6 motorcycles. During the next shot, the intersection is a different one.
On the "Bolt" TV series episode at the beginning of the movie, as Bolt is holding the car containing the guard from the bridge, we see the approaching helicopters, then we see the bridge as seen from the approaching helicopters. From that perspective, there is no car hanging from the bridge.
Near the end of the movie, Penny is getting ready for the TV show episode. You can clearly see that the cables behind her are taut. In the very next shot, the cables have slack in them and they are being pulled taut.
In one of the movie's early scenes, set in the animal rescue center where Penny adopts Bolt, a poster can be seen with the year 2008 written on it. Yet, in the next scene, which according to the film is taking place five years later, Bolt can be seen reading a magazine dated March 2008. That would be the same year Bolt was adopted. This is an obvious impossibility.
When Penny takes a Polaroid picture of herself with Bolt, Rhino, and Mittens at the end of the movie,
Mittens was sitting on the couch with her head facing Penny's mother and with her rear end facing Rhino
before, during, and after the picture. When the developed picture is displayed after Penny leaves the
house to play with Bolt outside, Mittens' head is now next to Rhino in the picture.
Errors in geography
When Bolt is in New York City, we can see a pedestrian "WALK/DON'T WALK" sign. In New York City, those signs show a white walking character (walk) and a red hand (don't walk).
The scene in which Mittens tries to get Bolt to stay in Las Vegas to live takes place in a desert-type field, not far from some alleyways - presumably south of Mandalay Bay based on the background shots. While it's true there are some dirt lots south of Mandalay Bay, there are no alleyways close to them. Likewise, this desert-type area seems to stretch on endlessly, but there are no empty lots that stretch on this far in the area - as the area being occupied is (in real life) surrounded by roads and hotel/casinos on every end.
The roll-up door on a U-Haul truck cannot be unlatched from the inside.
The CSX diesel locomotive pulling the train that Bolt swings onto from the bridge is an EMD SD70M, #432. CSX did not number any of their SD70Ms in the 400s. CSX numbered their SD70Ms from 4675 to 4699. CSX locomotive #432 is, in reality, a CW44AC (CSX's designation for an AC4400CW).
At the time the film was made (and still today) all U-Haul trucks have Arizona license plates.
Bolt calls Dr. Calico "The Green-Eyed Man". Even though a great percentage of people think the opposite, dogs are not actually colorblind. However, they do see colors differently than how humans do. Dogs don't seem to be able to see reds or greens very well, so their world probably exists in various shades of yellow and blue. Because of this, there is no way that he could recognize Calico's eye as green. However, he would have heard Penny calling him "The Green-Eyed Man" a lot and is likely to have repeated this. Yet, Bolt is able to recognize blood as "this red liquid" when he injures himself.
When Penny is loaded into the ambulance, the cot is placed towards the passenger side of the ambulance. The cot retention mechanism in an ambulance is on the driver's side. In a following shot through the open doors of the ambulance, it also shows the cot in a raised position. Cots are collapsed when placed in an ambulance.
Incorrectly regarded as goofs
At a shelter, a tank of helium explodes. While helium itself is not flammable, the helium tank is filled with a compressed gas. When the valve gets knocked off the helium tank, the compressed gas rapidly escapes and turns the tank into a missile. The tank flies uncontrolled out of the building, and hits a sign post, knocking it down. The sign post falls onto a truck carrying a larger tank (presumably a fuel tank), which can be seen correctly labeled with a flammable liquid placard.
In the "Cliffhanger" scene, Penny rolls a penny to distract the guards. The closeup of the back of the penny is missing Abraham Lincoln sitting in his chair. This happens frequently in cartoons. Since there are laws against depicting currency too realistically in reference books etc., the animators are being overly cautious to avoid accusations of counterfeiting.
The director is upset because a boom microphone is visible in the frame and "the dog could have seen that." Regardless of what the camera captured, the microphone and its operator were out in the open on the set itself, where Bolt could have seen them during filming, even if they were edited out later.
Near the beginning of the film, Calico is sitting with a cat on his right shoulder. Their reflection is shown in the glasses of a man directly opposite. The reflection shows Calico and the cat in the same position instead of being reversed, as a reflection would be.
When Mittens is on the tree branch and is still tied with the leash to Bolt on the ground, she walks forward and loops the leash onto a broken branch. The leash runs down behind the main branch on her left side, there is a smaller branch ahead of her sprouting out on her left (we see this in an overhead shot.) When she moves forward to loop the leash on the broken branch, the leash somehow moves through this branch on her left instead of getting stuck behind it.
After Bolt had fallen into the cardboard box it is carried away with a smaller box and placed into a truck together with other boxes. When comparing the bruises and cracked edges of the boxes one realizes that the boxes are only resized copies of each other.
When the man hears Bolt's barking coming from a shipping box, he takes a knife and slices the tape that goes across the top of the box just once. However, in the very next shot, the tape is clearly shown as having been cut along the sides as well.
In the beginning of the movie during the chase scene, when Bolt places the time bomb on the chasing henchmen's helmet, Penny's image is reflected on his visor. After he takes the time bomb down, Penny's reflection on his helmet visor is gone.
In the Uhaul truck, just before Mittens is about to hit Bolt with a baseball bat that she found in the truck, she falls backwards, dislodging a box. This box falls on Bolt and is filled with Styrofoam, and apparently nothing else.
The container train is obviously moving at speed on a main track, but lacks a rear-end marker/telemetry device required of all trains authorized for mainline movement.
At the end of the "dog-face" RV park montage, there's a slow pan across the park. A grill is visible in the foreground, but the smoke coming from it is frozen in place.