Since the dawn of the Transformers brand, a variety of unconnected media has conspired to create multiple continuities, even within individual franchises. The most famous such continuity split is the divergence of the original cartoon and comic, which contributed sometimes similar but ultimately irreconcilable versions of Generation One. While the most prominent continuities are well known, there exist many "micro-continuities": continuities about which only very limited information is available, yet which manage in that small space to be incompatible with the major continuities.
Continuities that exist in a very small number of works that may share an apparent single continuity, such as the Ladybird or Find Your Fate Junior books. Some continuities may even appear in only a single isolated work, such as the Transformers Beast Wars: Transmetals video game.
Although usually small and insignificant in the wider scheme of things, such tales can contain interesting or unique takes on certain characters or situations—for example, providing actual stories in which Ultra Magnus and Galvatron spent a prolonged period as opposing leaders, a status quo hinted at by much of the lead-in and post-movie product advertising but which was ultimately never realized in the major fictions.
Probably the most underdeveloped medium in Transformers fiction, prose stories are considered to be offshoots from their parent continuities (as is often the case with the expanded universes of even prolifically novelized franchises like Star Trek). However, the prose stories that were included in the Marvel UK annuals are a notable exception, as most of these are usually treated as part of UK continuity.
The Find Your Fate books are, by their very nature, micro-continuities (or, if you want to be pedantic, they contain multiple "nano"-continuities within them), since the various outcomes frequently involve the deaths of major characters.
The success of Dreamwave inspired a small, short-lived boom in Transformers prose fiction. The Keepers Trilogy was intended to be set in the Dreamwave continuity, but as Dreamwave was not really involved in their publication and subsequent Dreamwave comics made no explicit reference to them, it is a matter of taste whether the trilogy is part of the Dreamwave-verse proper or is a micro-continuity offshoot.
The prose anthology book Transformers Legends is more cut-and-dried at first glance. The foreword by editor David Cian explicitly states that the short stories in the anthology do not have canonical status in their respective continuities, and are "what-if" tales. For some of the stories, such as "Paddles", "Fire in the Dark", and "Lonesome Diesel", it is quite clear from their inconsistency with pre-existing continuities that they are micro-continuities.
However, other stories in the volume (such as "Singularity Ablyss", "Parts", "A Meeting of Minds", and "Redemption Centre") fit nicely into their respective continuities and (were it not for the editor's caveat) could easily be canon. It is thus debatable whether these stories are also mere micro-continuity offshoots or something more.
While never truly represented by any narrative fiction, some micro-continuities arise as the result of discrepancies between the toy lines and characters' portrayals elsewhere. In Generation One this was often limited to individual characters' appearances varying drastically between toy and cartoon (and, by extension, most other media). Prominent examples of this are Jetfire and Ironhide.
Implied continuities can also include discrepancies in on-package bios, such as Galvatron being described as merely "Decepticon City Commander" and possessing a lower rank than his unspecified superiors (not to mention the fact that he is nowhere said to be a reformatted Megatron, probably to avoid spoiling the movie). A more striking example of such differences implying the existence of whole new continuities occurs in Beast Wars and Beast Machines (see below.)
Some toys exist in a complete continuity vacuum; the only indications as to the nature of the universe they inhabit that can be gleaned are from their on-package bios.
Japanese exclusives are particularly prone to this, especially some of their more bizarre cross-promotion toys such as Pepsi Convoy, the Takara Sport Label Optimus Prime and Megatron figures, who transform into miniature Nike sneakers, or Takara Music Label's Optimus Prime or MP3 player Soundwave. Is one seriously to consider these characters part of a mainstream version of G1 continuity as their bios imply, or does one relegate them to weird little micro-continuities in which Optimus has an insatiable desire for signing endorsement deals? YOU decide.
The Machine Wars toy line is the best example of bio-only implied continuity as, very unusually, it represents an entire line (albeit a very small one) which possesses no official fiction in any form save for the toy bios, in which story hints are limited mainly to the existence of Megaplex and a few peculiarities about Thundercracker. Given the lack of any other story material, whether the differences/character development with Thundercracker imply a whole new micro-continuity or are viewed as new developments within an existing continuity falls solely to personal preference.
Beast Toylines vs. Shows
Unlike G1, the Beast Era has not featured major divergent continuities, leading (at least for most of its existence) to a fairly unified canon.
However, due to the high cost and time constraints of a fully CG-animated series, both Mainframe Beast shows were limited in the number of characters that could be included. They are remarkable amongst the Transformers franchises in not showcasing nearly every available toy as a character in the show. As a result, the main Beast Wars and Beast Machines fiction-depicted continuities feature only a limited portion of the overall number of toys/characters created, and furthermore the tight storytelling and premises of the shows leave little room for their inclusion in an "off camera" capacity (although see below: "When is a micro-continuity not a micro-continuity?"). An additional discrepancy in Beast Wars is that several characters, such as Waspinator and Rhinox, were featured as Transmetal toys, but were not upgraded in the cartoon. (Note that IDW's Beast Wars Sourcebook attempts to provide a rationale for these missing Transmetal bodies, as well as the bat and crocodile forms of Primal and Megatron, at least in terms of their own version of continuity.)
One can either postulate that the toy line itself implies a micro-continuity in which the full number of toy characters coexisted, or one could attempt to reconcile these characters with an already existent micro-continuity: that of the pre-cartoon on-package bios and mini-comic...
The "G1 Beast Wars"
On-package bios for the first waves of Beast Wars indicated that the Beast Wars took place on present-day Earth, and that Optimus Primal and Megatron were just G1 Optimus Prime and Megatron in the latest of their long series of reformatted bodies. This storyline was showcased in one installment of "limited fiction," a comic which was included with the bat Optimus and alligator Megatron 2-pack.
Although later bios would reflect the universe established by the Beast Wars cartoon, these first-series materials create a micro-continuity that features a bat-mode Optimus Prime(al) leading troops that include the likes of both Rattrap and Razorbeast against an alligator-mode Megatron and his minions, such as Tarantulas and Iguanus, stalking their secret genetic labs and duking it out for the fate of modern, urban Earth. It is then open to debate whether Optimus and Megatron subsequently "upgraded" to their gorilla and T-Rex modes (the comic certainly implies that Megatron plans to), or that later waves of show, non-show, and even Transmetal characters are featured in this micro-continuity.
Crawling with Maximals
The Beast Machines toyline contained many toy-only characters—Maximal, Vehicon, and "other"—who were again fairly incompatible with the tightly plotted continuity of the cartoon. A similar "implied continuity" can be postulated that would include these extra characters in an alternate version of events that supported a larger cast.
When is a micro-continuity not a micro-continuity?
There are some continuities which have attempted to explain retroactively the presence (or rather absence) of the non-show characters in both Beast Wars and Beast Machines. 3H's Wreckers comics and associated projects attempted to fill out much of the Beast Machines gaps in a workable fashion, while IDW has tackled virtually every toy-only Beast Wars character in Beast Wars: The Gathering. However, these two approaches contradict each other, and neither have (as yet) provided expansive storylines. Whether one deems these stories to be part of the larger show-based canon (despite contradictions), individual "complementary" continuities, or indeed just larger-than-usual micro-continuities themselves is, like most things, up to the individual fan's taste and personal canon.
By the same token, the comic-book fictions for Generation 2 and Transformers Classics present timelines that diverge from the U.S./U.K. Marvel comic, each representing full toy lines. This may be compared with Machine Wars which is apparently a continuation of G1 but may or may not exist (later) in the same timeline as G2. Whether such examples of divergent offshoots of larger continuities should be classed as micro-continuities (in spite of toylines and many issues of fiction) or be included with their "parent" continuities as branched extensions is, again, a matter of taste and personal canon.