Okay, coming later tonight in 4.063:
* Fixed a bug in the prior version that was causing waves in the intermediate tutorial to come into play not belonging to the AI player (and thus be unhittable by the human player, as well as treated as allies -- so they would attack AI ships automatically, etc).
** Also made it so that existing saves with those "Allied ships" in them would convert those ships over to the AI appropriately.
Thanks, whiskeypriest!