In a rare multi-million dollar live action example: the live action Transformers movies, which in spite of utilizing Industrial Light and Magic. Still ends up having several glaring moments of this:
Three examples occur during Revenge of the Fallen. In one scene during the Shanghai battlenote the chase with Sideways, to be exact, Mudflap and Skids switch voice actors. Two more appear during the desert battle - In one instance, Ironhide ejects his guns at one point and regains them in another and the CG predator drone shown in the film doesn't look like anything like its actual counterpart, which also happened to be used in the film.
A couple more occur in Dark of the Moon. In the standoff between Ironhide, Sideswipe and The Dreads, Ironhide drops his guns. When he gets shot however, his CGI model shows them attached onto his back instead. After that, all other shots during the standoff and beyond keep them absent. Bumblebee's paint job is also noticeably off, with his robot mode having a different pinstripe design then his car form.
The Asylum, who falls into this with so much gusto that it's not funny. With Mega Piranha, 100 Million BC and Transmorphers as 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, specifically 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 said scorpion gets a close up on its face. In that it looks nothing like the stop-motion version of the beast that Willis O'Brien animated.
The Xenomorphs in the Alien vs. Predator movie 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 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 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 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 (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. Having gotten 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. Kong's 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. But whenever the robot is used, it has green scales (the suit had a greyish-black tint) 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. No, it didn't look anything like the suit.
Watch Mighty Morphin Power Rangers: The Movie, then watch the series proper. Notice that the CGI Ninja Mega Falconzord of the former looks absolutely nothing like the costume from the latter. This is apparently because they modeled the CG version after a smaller version of the toy.
An "In-Universe" example: Terminator 2 during the T-1000's death scene.
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.