Funny, that's exactly what I was going to say. It's perfectly possible the dealer couldn't get access to the updated firmware required after the new battery is installed. If they can't download the software, they shouldn't install a new battery.It's quite possible that when they say "GM is having software trouble right now" that they're not referring to the software in the vehicle but rather some sort of issue in GM's server network that's preventing them from downloading the required software to the car. Or even some update of the software that they use in the shop to do that downloading.
It would be wise not to jump to any conclusions.
Also, the person giving you the message isn't likely an IT person that would be able to correctly articulate the nature of the "software issues" (nor would they need to).