Couldn't believe it when I saw it. I'm not sure what the catalyst was, we happened to hit war rank 6 at the same time.
Was a 2v2 on Ziggurat, pantheon, with 1 AI on the opponent team. I had just destroyed several of their towers. Suddenly, a few of them spontaneously respawned, right in front of me, with full health.
I've attached the replay: The incidient occurs between 12 minutes and 13 minutes in.
http://www.2shared.com/file/9312757/49d19e02/Towers_Regenarting_Bug.html
Edit: Pacov seems to have looked into this and concluded that certain towers were not spawning until late in the game. I originally thought certain towers that I had destroyed were regenerating: this does not seem to be the case. Instead, certain towers seem to not exist, and then suddenly come into play.