I have thought about it, and I think this issue only affects VaultWiki on XenForo. This is not a new bug by any means; it should date back to Gamma 3, when VaultWiki first started using XenForo's moderation popup. Since VaultWiki uses its own moderation code after you submit the popup, the bug lies on the VaultWiki side of things.
You should be able to workaround the issue for now by choosing "Deselect Pages" from the drop-down whenever it still thinks something is selected that you already performed an action on.
I have confirmed that this occurs with other moderation actions too, not just delete. After the action is completed, the pages are still selected on the next visit to the list.