God-Created Canon Foreigner: Most of the anime-original characters were created by Hiro Mashima himself; the ones who appear in the "Key of the Starry Heavens" arc are even accepted as canon thanks to its Continuity Nod present in Chapter 282 of the manga.
The Other Darrin: The English dub, as good as it is, is not completely immune to this. Corey Cleary-Stoner replaced Michael Chinnici as Jet starting at season two and Lindsay Seidel replaced Kayla Carlyle as Romeo only halfway through season one.
In Japanese, Mai Nakahara, Juvia's actress, briefly replaced Satomi Arai as Bisca during the Fighting Festival arc, with Arai returning to the role soon after.
Also in the dub, Magic Council member Leiji went from Jim Johnson to Keith Kubal when the new council is formed in episode 96.
Plue was voiced by Majken Bullard in season one before being replaced by Monica Rial for the rest of the series (she is also Mirajane).
Mashima mentioned in Volume 10 that he once thought of Erza's entire adult life being All Just a Dream of young Erza, but decided against it when he realized what that would mean for the entire rest of the series.
Considering the problems she has as an adult (not the least of which is that the love interest she relied on so much as a child is Brainwashed and Crazy), this would have some serious implications for her mental state if it were true.
Her friends also were supposed to be the Quirky Miniboss Squad of the arc, rather than have a Bait and Switch with Trinity Raven. When he was writing their backstories Mashima decided that he liked them too much to make them serious villains.
Similarly, Erza's original character design had her as more of a Nubile Savage than the Magic Knight we know her as. Mashima's idea for her character was simply "a woman badass enough to scare Natsu" and everything evolved from there.
Makarov was supposed to die during the Tenrou Island arc.
The anime was officially going to end after the Daphne filler arc, which is why most of the passing references to Gildarts were left out. It proved more popular than expected so it continued.
According to the Q&A section of volume 22, Erigor was supposed to appear during the Oracion Seis arc in the manga, but was ultimately cut out. The only bit that was left in was a brief mention at the start of the arc before Team Natsu's departure. However, he was added into the anime version of the arc.
The name Oración Seis was originally only used as a placeholder for another title Mashima was trying to come up with, but he ended up going with it when the deadline came too close for comfort.
Mashima always intended for Faust to be Makarov's Edolas counterpart, but was forced to exclude it from the manga for reasons unknown. He was glad to see that the anime included it, but complained that their shared actors (Shinpachi Tsuji and R. Bruce Elliott) made the connection too obvious.
Cosmos was originally named "Fione", but her name was changed because it sounded too similar to “Fiore".
Before The Reveal that Doranbalt is a council agent pretending to be a member of Fairy Tail, Mashima considered making him an actual member of Fairy Tail, Grimoire Heart, or even Tartarus.
Edolas Gajeel was intended to appear in the manga, but was forced out for unknown reasons.
Word of Dante: Everyone treats it as a well known fact that Lucy's mother died on July 7th X777. If you actually look through the series you might notice that while she did die that year, there's no mention whatsoever of the exact day or even month she passed away.