I don't believe the genetics of crossed beaks have been well studied. To me the following logic makes sense.
If both parents have normal beaks but they throw crossed beaks, it must be one or more recessive genes causing the problem. I have noticed in the past that crossed beaks come most often from closely bred lines (closely related parents), but not always. So my best guess is that your male bird and one or more of the females in his pen are at fault. My advice is to test your females individually with this male by penning them seperately and rotating the male, marking which eggs come from which hen, then toe-punching or otherwise identifying each chick that hatches, and raise them until the crossed beaks develop and you know which hen or hens are responsible. Once you know who the culprits are cull them, including the rooster, and all their chicks by making sure they don't re-enter the gene pool. The easier way would be to cull all the birds in that pen immediately if you have adequate replacements. The responsible thing to do is make sure the problem does not become someone else's. In the past I dealt with the same problem in wheaten bantams for years. It helps to select for breeders those birds with shorter, stout beaks, whose lower mandibles are well fitted to the upper ones. If you can see daylight between the upper and lower when the beak is closed you are seeing a carrier of crossed beaks in my opinion.
