 (Babylon 5 and Farscape fans are familiar with "We had to finish out the epic story HOW fast?" syndrome.)  Because some storylines fizzle and others appear that work better.  Because two characters intended to pair up at the beginning have more chemistry with different characters instead.  Because the audience complains.  Because the audience isn't the one desired.  Because the head writer got (or lost) religion.  Because the publishing company wants to turn the trilogy into a twelve-book deal and the original plot barely covered two books with padding.  Because the showrunner thought one thing and didn't relay it to the rest of the writing staff, who went in completely another direction, and when the showrunner states in interviews, "Obviously, ABC," the audience who tuned in to the actual series are all united in their confusion of, "But, but, did you not notice XYZ?"  Because the producers become angry at the actors or the audience or the show itself, or they get bored with the book series, or because they get hit by a car and add the experience into their epic fantasy series.  (Stephen King, I'm looking at you.)

Ideas change, and what the author says one day may not be what's in the final print tomorrow, and may be a whole different story next week.  That goes for what the actors say, too.  Even when they're on stage at a con saying, "Oh, I totally meant LMNOP when I moved my eyes like that."  Later scripts might declare that the character was in fact replaced by an evil android during that scene.  You never know.

Authorial intent can become fanon.  

When two or more fans agree that someone happened which wasn't shown, or that something which was shown happened for a particular reason that isn't flat-out stated in the canon, this is fanon.  Fanon is a shared fannish reality of a source material.  Sometimes the fanon is closely related to the source.  For example, most "fade to black" scenes in a television show are intended to imply that the characters in question then went on to have sex, and in general, the fans of that show agree with one another (and the producers) that sex did in fact take place immediately after the cutaway.  However, if no sex was shown, and the characters in question did not mention it again, it is also possible fanon to assert that in fact they broke apart from their kiss, exchanged passionate handshakes, and then played Parcheesi for the rest of the unspecified time.  (Doctor Merlin suggests this is not the interpretation most suited to later character interactions in most cases, but remains possible.)

Multiple fanons exist.  One group of fans will swear that when these two characters are in a room together, their interactions are stilted and difficult because they hate each other.  Another group of fans will declare it Gospel truth that the difficulty is because the characters want to shag like bunnies. 