Those are all questions that unfortunately I cannot answer with any certainty. When it happened to my guild we were compensated with war tokens and gold chests if memory serves. I'm not a 100% on that as it happened some time ago. We were the 1st place guild in war for months, so I do remember the compensation was nowhere near what we would have received in rewards.
There are several theories concerning this glitch. There is some evidence that when someone is booted or joins the guild that both the person that joined/booted and the person doing the accepting/booting are dropped out of the war roster causing the guild to drop below the minimum required for registration. There is also another theory involving ties but I admittedly don't fully understand it, so I'm not qualified to explain it. Regardless, I don't think there is anything you can do about it.
The concensus among players and GS I have talked with believe it best to wait as close to war time as possible to register. I'm not sure if it will help, but I don't see that it can hurt.
Lastly, in regards to you filing the ticket for the whole guild... That will probably work, BUT in my experience the more players you have compla... er... corroborating the event the better.
Good luck! I hope you get compensated well.