EDIT (30 May 12:40 GMT+0): We have now forced the update and this issue should be resolved!
EDIT (30 May 11:40 GMT+0): We have found out that the issue is caused by the known bug related to Thoth Amun's or Delilah's minions. If the attacking or defending team has either of these heroes, the battle will result in 0 points.
We are aware that some players are currently experiencing an issue where victorious Alliance War battle ends up with 0 points and the opposing team being still alive.
We are currently investigating the issue and hope to get it resolved soon. Our apologies for any inconvenience caused!