I do not recommend breeding her. Whatever the cause, you never want to chance this being genetic. If it's genetic, her offspring will be way worse than her and will likely need to be culled or tube fed. (And if you’re selling these chicks, it could hurt your reputation.)
It sounds like it previously had crossbeak and it was just missed. The mess on her beak may be linked to the crossbeak. Crossbeaks are messy eaters and don't always keep their beaks as clean as they should.
Do you know what the feed had in it for nutrients? Sometimes the lack of specific...