Transformers: Revenge of the Fallen contains three notable examples. In one scene during the Shanghai battlenote the chase with Sideways, to be exact, Mudflap and Skids switch voice actors.
During the desert battle, Ironhide ejects his guns in one scene, yet regains them the next.
Also from the desert battle- There's a predator drone that switches between a CG model and a real drone. The CG model looks nothing like the physical model. Which is further compounded by Stock Footage from the first film, which used a completely different drone altogether.
Transformers: Dark of the Moon, during the standoff between Ironhide, Sideswipe and The Dreads, Ironhide drops his guns. When he gets shot, his CGI model shows them attached onto his back instead. From that point on, from the rest of the standoff until he dies, they remain absent (as they should be). Bumblebee's paint job is also noticeably off, with his robot mode having a different pinstripe design than his car form.
Also from Dark of the Moon, Soundwave's voice can be heard, and seen, coming out of Barricade during Que's execution. Whether or not this was intentional, or just an animator not paying attention remains unclear.
Sentinel Prime's cape briefly disappears during his fight with the Autobots at the end of the film.
The Asylum, who falls into this with so much gusto that it's not funny. Mega Piranha, 100 Million BC and Transmorphers are quite possibly the worst cases. It's a damn shame when you consider that Synapse FX (responsible for the effects in Transmorphers) actually made fairly detailed and complex models (roughly about as complex as Wheelie or Frenzy from the above-mentioned Transformers films) of the titular robots◊.
The Matrix Reloaded. Watch the "Burly Brawl" scene. Most of the fight is CGI and if you can get a close enough look at Neo's face you can tell that it looks absolutely nothing like Keanu Reeves - though most people probably wouldn't see it the first few times they watched it.
Happens in The Black Scorpion whenever there's a close up on the eponymous monster's face. It looks quite different from the stop-motion scorpion that Willis O'Brien animated.
The Xenomorphs in AVP: Alien vs. Predator switch between animatronics and CG. While not necessarily a bad thing in and of itself, it is worth pointing out that the CG Xenomorphs have an extra joint in the ankles, a trait that the costume lack.
While Dragon Ball: Fight for Victory, Son Goku! is largely based upon its source material, some of the non-human characters, mainly Puar and Turtle, ended up receiving slight color changesnote Turtle having an obvious seam on his beak and Puar being a plush toy notwithstanding. On the poster however, is a rather odd-looking Shenron wearing sunglasses for reasons unknown (In the movie itself, he fares better design-wise, but is depicted as a glowing green outline).
Not even King Kong is immune. Close up shots of the beast in the 1933 film involved a mechanical face and hands that gave him a more cartoonish look. This tradition continued in the 1976 remake, in which the 40-foot tall robotnote itself a (widely publicized) effects failure looks absolutely nothing like the suit.
In the first Spider-Man film, the costumes for both Spider-Man and Green Goblin seem to lack certain details when shown as CG models. Specifically, Green Goblin's helmet does not have Norman's mouth - something that the actual costume does show. This fault ends up carrying over to most of the action figures based on that design.
Most of the original Godzilla films do this during any scene taking place in the water by using a costume from an earlier film instead of the costume built for the current film (so as to not damage the current suit).
This was especially noticeable during the late '60s and throughout the mid '70s, when the budgets were very low. It got to the point where one suit started to fall apart during the filming of Godzilla vs. Gigannote it's worth pointing out that the aforementioned suit, which was in use since 1968, was retired after filming. Other major examples include:
In both Gojira and Godzilla Raids Again, the monster's close-ups are operated by a hand puppet that isn't an exact match to the suit, especially with the eyes and hands. Meanwhile, the "photo" (really a painting) that the professor uses to identify the monster looks nothing like either. In Raids Again, the hand puppet for Godzilla actually looked creepy when he burns Anguirus after defeating him.
In King Kong vs. Godzilla, the stop-motion model used for Godzilla's infamous dropkick only resembles the suit very slightly. The Kong puppet used for closeups and the suit itself also qualify. Likewise his arm prosthetics, which keep disappearing and reappearing depending on the scene.
For The Return of Godzilla, a 20 foot tall animatronic was constructed and heavily publicized, much like the above mentioned 40-foot Kongnote but unlike Kong, it actually worked. Whenever the robot's used, it has a greenish tint to it (the suit itself was greyish-black) and a face that would remind one of the Live-Action Teenage Mutant Ninja Turtles. The positions of the eyes are also radically different from the suit's.
The suit itself is also different than the later Heisei entries, as it was originally made for another stuntman in mind.
In a few scenes of Godzilla 2000, a CG version of the titular character was used. It doesn't look anything like the suit.
The costumes for Zed and Goldar are also completely different than what they normally look like on the TV show. Though in the former's case, this helps enhance the creepiness of the character.
An "In-Universe" example: Terminator 2: Judgment Day after the T-1000 is damaged by its freezing, it keeps going off-model. In the director's cut of the film, this spoils its impersonation of Sarah Connor.
in a more meta sense of this trope, expect to see this with the animatronic Arnold in a few scenes of the second film. Such as near the end when he fights the T-1000.
Likewise, the robot double of Arnold shown in the first film looks more chubby around the cheeks and chin. And he develops an inhuman rubbery sheen.
The theatrical release of Star Trek: The Motion Picture has some horribly drawn mattes of the USS Enterprise's saucer when Kirk and company emerge from it to walk over to V'Ger. This was fixed in the 2001 Director's Edition, which redid the scene to match Robert Wise's original storyboards showing the formation of the walkway, and used a CGI rendering of the original filming model of the Enterprise.
The CG model of Jurassic Park's lead T-Rex has a slightly squarer jaw than that of the animatronic.
In the first scene of the rock scorpion battle in the 2010 Clash of the Titans remake, said rock scorpion is missing part of its tail.
In the first film, the CG Iron Man suit had narrower hips than the real world counterpart.
This was (one of) the reasons why the third Ninja Turtles film was derided by fans and general audiences. It's not hard to see why considering the turtles suddenly sport cartoonishly big heads, bright colors and an overall frog-like aesthetic unlike the previous films. To say nothing about what they did to Splinter in that film.
Most Live action adaptations of the franchise tend to screw up the designs of the Turtles to some extent (such as the Coming Out of their Shells Tour, where the Turtles have two sets of costumes and Splinter becomes a hairball with limbs). But the best example is Operation Blue Line where the turtles look like their action figures (complete with unmoving mouths), which in and of itself is not the best idea. Worse still, they managed to screw the torsos of Michelangelo and Donatello up not just for a scene or two, but for the entire short.
The NeverEnding Story, while not having spectacular effects, did do them competently enough. The second movie was a step down, with Rockbiter getting a slightly brighter color scheme than the first film while Falkor's face is slightly changed between the two films.
Then you get to the third film, where they get complete redesigns to make them more "family friendly". Rockbiter, who now looked even more like a person in a rubber suit and gained several hundred pounds of girth, making him nothing more than a rocky version of Homer Simpson. Falkor somehow managed to get it even worse, now looking like a six-legged French Poodle with an incredibly doofy-looking face.
Night of the Demon (1957) - the title demon looks considerably different in long shot, medium shot and close up - much of that would be due to Executive Meddling that added in the close-ups where the director had only wanted it to be fleetingly seen (in the long and medium shots).
The Thing in the 2015 Fantastic Four film has a different looking facial construction in nearly every scene. It remains uncertain if this was supposed to be a stylistic choice or not.
A straighter example: The Human Torch's flames have a problem of appearing and disappearing at any given moment whenever he's supposed to be on fire.