I've noticed this on two occasions tonight. Once while using Rook's Hammer Slam, and again when using Sedna's Pounce.
The proceedure is thus:
First, initiate an ability that is intended to deliver damage to an enemy or creep. (I suggest using Rook's Hammer Slam for this proceedure, due to it's innately slow nature.) Now, BEFORE the attack delivers it's damaging payload, UPGRADE that specific ability in your demigod's skill tree. Your demigod will still perform the animation for your intended attack, but the attack itself will not deliver any damage.
From what I've seen, this is also possible if you command your demigod to perform an ability on a target that is presently not within range. As your demigod approaches the intended target on foot, upgrade the ability your demigod is about to perform. Again, the ability will perform 0 damage when it is finally delivered, unless the command is re-issued.
All subsequent attempts at using the affected ability will be unaffected by this bug.