We are having the same issue with being unregistered which really makes me feel it was a glitch because the 50% rule y'all are referring to is being misinterpreted.
This is copied straight from the guide:
Leaders, Champions, or Officers may register their Guild for the upcoming War every Sunday starting at 1 PM server time. A guild must have at least 10 members with war defenses set in order to register. Registration ends at 12, noon server time on Monday. If a Guild drops below 10 members or if more than 50% of members leave during registration, they will be automatically removed until they meet the requirements again (if necessary) and re-register."
This last line, reads that if a guild drops below 10 or loses 50% of its members during registration, it will be automatically removed from registration. This does not mean if 50% are opted out. It means if 50% leave the guild.
That being said, it makes me even more confident that it's a glitch. Also, this has happened before. Many months ago, right after Gree took over, and it was a glitch in their algorithms then. Hopefully it will be fixed before next week's war starts and they will compensate us for it. One can always hope, right?