It's not really a contradiction unless you take it out of context and don't examine the situation on the whole. The convoluted mess would mean that the story is centered around events that have taken place over the course of KoF 94-97, then 03-XI. To many people, how would they know which games aren't canon? Because of this, the KoF storyline is convoluted when you jump into the end of a specific saga that heavily borrows plot points from some of the oldest games in the series.
The story being short, adds to the above problem by not being long or involved enough to properly explain everything and make the player feel somewhat okay and understanding of the overall plot and what is happening and why. The two combined CAN happen and it's not a contradiction. They probably just failed to specify correctly on what they meant by convoluted. I didn't read the review but if they said "The series is convoluted" and "the game's story is short" then they did just fine there. The series' story seems more convoluted and hard to follow when the latest entry's story is very short and doesn't provide enough answers or backstory.
That being said...fighting games are never very strong in the story department so to judge a fighting game series that's lasted for over fifteen years now based on story, is a dumb thing to do, especially when KoF has a stronger story than Marvel 3. But I don't think IGN overall monitors who is reviewing what. The left hand doesn't know what the right hand is doing. There is more than one reviewer at IGN and the person who reviewed KoF XIII is probably not the same person who did UMvC3. If he isn't the same person, they probably got someone who does not care much for fighters to review KoF XIII or someone who doesn't know anything about them. If it is the same person then he is just a hater and loves Capcom. But game reviewers are mostly full of crap these days and are mostly interested in western games and frat boy games like Call of Duty. EGM is still good thankfully.
I just don't understand how you dock it down twice for the same thing with such a contradiction. How can a story be short and convoluted at the same time?