Author intent is the meaning or interpretation of a fictional work that the author had in mind when he or she was creating it.
Frequently in the various Transformers fictions, the author's intent ends up being unclear or even contradicted by the finished work. In these cases it is up to each fan to decide whether to accept the author's intent or the work as-released.
Sometimes the correct interpretation is obvious, but other times it ends up being a matter of debate. When the author's intent doesn't make it into the final product, can that intent still trump the "true" events as shown in the canon? This is an especially difficult question when one considers that the author's explanations, even if widely disseminated through the fandom, are still only known to a tiny portion of the fiction's full audience, which includes far more casual fans and children than it does devoted information-hounds.
Facts about the fiction that are stated/intended by the authors but never established in official fiction are often referred to as pseudocanon.
Optimus Prime's "Spark Holder" in Beast Wars
In the episode "Optimal Situation", Optimus Primal was shown removing what appeared to be the Matrix from Optimus Prime's chest. Instead of the Matrix's traditional crystal, this object contained a spark which Primal absorbed into his own body. According to Rhinox Prime's spark "has the Matrix with it." After absorbing the spark, Primal grew in size and attained his "Optimal Optimus" body. A parallel can be drawn between this event and the upgrade from Hot Rod to Rodimus Prime when he received the Matrix in The Transformers: The Movie. On the other hand, the idea of the Matrix housing Prime's spark was somewhat contradictory with previous fiction.
After this episode aired, Bob Forward and Larry DiTillio informed fans that the script for this scene had simply called for Prime's spark to be contained in an elaborate "spark holder". The animators at Mainframe Entertainment, in looking for inspiration, came across images of the Matrix and adapted that design, seemingly not realizing that the object they had chosen held special significance. The writers had intended for Primal's upgrade to be a result of holding two sparks, not a result of contact with the Matrix. Further, they encouraged fans to take Rhinox's line as being metaphorical, with comparison to the Matrix simply being a Cybertronian idiom for something extremely important.
How, then, is a fan to take this scene? Is that really the Matrix, boasting different properties than before? Comments from writers are certainly helpful information, but they are not strictly canonical.
This particular conflict was eventually retconned in the "Primeval Dawn Part 1" comic. There, it was depicted (both visually and through dialogue) that Prime's body "hides" the real Matrix behind a lookalike. This explanation also works because the design of the spark case in Beast Wars was significantly different from the original Matrix design, in that the colors were different and it lacked the finger holes of the original (though the Matrix design shifted frequently in the Marvel comics).