Something that should be edited in:
For every crystal a guild captures, they receive an 8.3% chance to win. Every crystal captured adds to the total and when time ends, the winner is randomized from these results.
This stands to chance that a guild with a 24.9% chance to win could lose to one of four other guilds with an 8.3% chance to win.
(Actually in this scenario, they have a greater chance at losing than they do at winning, they only have the highest individual chance to win)
The tl;dr is that even if your guild is organized and knows exactly what it's doing, you stand a good chance to lose given bad luck.