Maybe it's a little long story.
Maybe it's a little longer story.
Well, first of all, the placement of "story" at the end of the sentence is very strange. Either "it's" should be referring to the story as mentioned in a previous sentence, or you should say "Maybe the story is a little long/longer".
Secondly: "Maybe the story is a little long" means that you could, if you tried, shorten the story up and still cover everything you need. (Perhaps someone said "You rambled a heck of a lot in that story.")
"Maybe the story is a little longer" means that you arrived at the apparent end of the story but you're letting the listeners know that there's actually still something to be told. (Perhaps someone said "What, that was the end?? Awwww, I wanted something more to happen.")
Those are definitely ungrammatical. A little long and a little longer are both fine adjective phrases, but they can’t be used before a noun like that, I guess because of the determiner a in them. Similarly you can’t say:
Anything that appears before a noun like that has to be quite simple in structure.
However, an adjective modified by an adverb is fine:
Hellion is right about the difference between long and longer here and the other possible solution:
As a matter of style, I would say “Maybe that isn’t quite the end of the story.”