Transformers Generation One may have had a reputation of being this trope in both comic and cartoon formats, but it should also go with saying that the figures themselves are not immune due to their heritage of being from different lines:
Ironhide and Ratchet for instance, have proper heads in all non-toy related material, but their original action figures don't. This is because the original figures were made in Japan for a different purpose- before the concept of Transformers came into play. Those figures were meant to be "armor" used by human pilots, but the idea was shelved when the toys were re-worked into transforming robots. In fact, there are even Bot-con and fan surrogate modifications that can be applied to these toys to give them actual heads.
Some other noticeable ones include Swoop not being the same color as his cartoon model (he was in the predecessor line Diaclone however), many characters (Trailbreaker, Bumblebee, Mixmaster of the Constructicons) having mouthplates instead of proper mouths, Jetfire going from his VF-1 form to a generic jet between the toy release and show and Galvatron being grey instead of purple (This was corrected in a re-release in 2005).
Due to the difference in economic realities and lead times - a given 'Deluxe' sized toy will be twice the price and released later in Japan - toys released by Takara will usually have more paint apps and generally be more show accurate compared to their Hasbro counterparts. This can range from car stripes being a slightly different color to a totally new deco.
Recently (2010-2012) third party companies have started developing cartoon accurate figures or accessories that fit specific toys or toylines. The "heads" for Ironhide and Ratchet are an example. Some of these companies went even further and released knock offs of the original toys in their cartoon accurate color (KO Diaclone Blue Swoop being an example related below). There's a lot of controversy in the fandom about this, to say the least.
Some of the earliest toy commercials (which included animated segments) were off-model in a different way: Technically, they were on-model, but to models completely different from those used in the cartoon. For example, Megatron's early model was based on a prototype of the Diaclone toy that would become Megatron, resulting in it having a black head and some other differences. Jetfire was actually based on the toy, rather than having the "Skyfire" design from the cartoon.
Even though this was intentional, the characters in the first three BIONICLE movies (touched upon in the Animated Films section), look nothing like the toys.
An issue regarding a discrepancy between what's on the box versus the figure itself: the chest-piece that Hydraxon is shown wearing in just about every piece of promo material simply doesn't exist — it's a slightly remodeled version of the "webbed Piraka foot" piece, but the toy has the regular one.
Bizarrely, the instruction booklet for the 2005 Oohnorak set uses a short ball-socket connector to attach the front legs to, but the toy comes with the longer version. So the toy looks a bit different than the picture in the booklet.
The instructions and promo pic for the Sea Spider combiner model can't seem to agree whether to use the two orange see-through "eye" pieces as claws on the spider's back legs or as its mandibles. It's uncertain which one is off model, though.
Krekka's boxart places his eyes into what would probably be his nostrils... the artist either wasn't told that his real eye is supposed to be that red LEGO piece next to his head, or the decision to make it so came after the image was done.
Keetongu's left thigh armor is put on upside-down on his boxart.
Similarly, the armor piece on Toa Ignika's right upper-arm has the wrong end facing up on the picture on the back of his box.
2007 was the year when LEGO made a point of not having their canister-sets be clones but design each with a unique built. The playsets of that year ("normal" LEGO sets with Bionicle Minifigures) however all used the same basic bodies for the characters, and only produced six headsculpts for the twelve characters. Most baffling of all, some of the sets gave even those characters the wrong head who've actually had their own sculpts.
Two of the Toa Inika figurines (namely Hahli and Kongu) released as part of a '06 Nestlé cereal promotion looked nothing like their true figures. They don't resemble any character, in fact. Here's "Kongu"◊ and here's Kongu◊.
Radiak's CGI promo image◊ has a twisted torso with the limbs and head not even connected to it properly. Looks like someone moved it to the side for the render, but left everything else where it was.
In some of Kopaka's CGI images (made available on promotional disks in 2001), he's missing many of his gray parts, like his gears, his connectors, and his head. His mask is quite visibly floating in the air above his neck. Most early promo art suffered from weird clipping and rigging errors as well, especially with regards to the toys' "joints", seeing as they mostly had rigid limbs with purely decorative "pistons" that never looked right when depicted as bendable arms and legs in CGI (special mention going to Lewa's painfully deforming left arm). These problems were later mostly ironed out with more articulated toy designs and CGI advancements.
About half of the 2005 Toa Hordika Minifigures have their arms mirrored (should be oversized right arm and puny left arm for all of them), and Onewa's figure has huge, protruding cheeks. On boxart, many of them also have their eyes misdrawn.
Usually invoked with Plush toys due to their chibiness, which is often shown with a lack of or simplified facial features such as eyes or noses.
There are many toy lines based on films and video games that feature notoriously bad likenesses to the characters they are supposed to be based on, even as of late with more advanced scanning and sculpting techniques generally making it easier to duplicate the likeness of an actor or computer model in action figure form.
This action figure◊ of Gerry Lane from World War Z is said to look as much like Brad Pitt as the film resembles the book. It's not even remotely the same haircut, and the less said about the eyes the better.
The Hawkeye figure from the Avengers Assemble line. Since it's just a repaint of the Jeremy Renner Hawkeye figure from The Avengers, it just looks like movie Hawkeye with some purple paint splashed on his costume, rather than his actual outfit from the show.
This is a common side-effect of cheap or knock-off toys. Especially noticeable in the ones that Ashens tends to review.
Neither the plush toy, or doll (Which is creepy in its own right) of Vanellope von Schweetz have the exact bits of candy in their hair. The plush toy for instance, actually has less candy; and both have the wrong color mints (White & red, instead of the green & brown in the film proper). The eyes are also wrong on both as well.
This page (as well as several pages linked on it) details how various toys and such based off of the Sonic the Hedgehog series have gone wrong, generally in this way.