Guild War battles should now be fixed, again. We apologize for the inconvenience but the bug was a bit tricky to track down. It should be back up and working as intended.
The current wars will end when the season timer at the top hits 6 days left (as of this post, about 22h left) and we are looking at a permanent fix that would prevent this from happening again.
Thank you for your understanding and support!
Happy battling :)