Warre originally designed his hive with the notion that the beekeper would at minimum only need to interact with the hive two times a year: once in the Spring to nadir empty boxes to the bottom, and at the end of summer to take off the top boxes filled with honeycomb. While some keepers like to be more interactive with their hives, the Warre hive is designed to be as hands-off as you like. In this situation, you have the opportunity to try that out, at least within that particular box. this next season, as you add boxes to the bottom, and eventually take boxes off of the top, you will be able to remove the honeycomb, utilizing the Crush-and-Strain.
In the future, you may want to consider some preventative maintenance, when your bees build into their first box, and when they build down into a new box.
--About one week after they start building into a new box, do a hive inspection. The new comb they will have made is pliable (and weak). If they are beginning to cross comb, this is early enough to manipulate the comb into a straighter position.
-- You can CAREFULLY twist and adjust the malleable comb with your gloved hand. Some of the comb may be sacrificed while straightening up the cross comb, but better now than later.
-- Be careful not to adjust the comb on a hot day (over 85 degrees fahrenheit). Much of your attempt will end with clumps of fallen comb
-- Make certain to consider gravity when adjusting comb. Anytime the comb is not perpendicular to the ground, it has a greater chance of warping and collapsing.
This may sound a bit complex, but if it is done around a week into a new box, the amount of comb is small enough that it isn't overwhelming.
Once the comb is straightened, they will continue to build straight... MOSTLY. Occasionally, they may slightly cross comb on the edge bars. This is usually quite simple to adjust... as long as you catch it before they've built the comb completely out.
I hope that helps!
Andrew at Bee Thinking