This isn't a new bug in the beta, but it hasn't been fixed yet. A while back, structure templates were changed so that you couldn't target them to destroy them. However, AoE effects/damage still apply. Just get one Crusader with Vengeance researched near a bunch of 0% templates, and watch them all go boom. Something like Malice works too. The templates are affected, and take damage when a completed structure or a unit nearby take damage.
