Since no one responded to this, I just reloaded save from about 2 hours before this point and played through the battery again. Didn't get two discs this time and it worked.
Still - there's apparently a way to get two discs, so that sounds like a bug. I vaguely remember clicking around on the dialogue options when you click on the pool very quickly or maybe even clicked on the pool again very quickly to get the dialogue again, which may have gotten me the second disc.