This seems to be a bug either with vanilla or Spigot (more likely the former). It may be worth investigating whether this happens with a completely vanilla server.

Since when does Minecraft allow IPv6 connections?

Was the IPv6 connection on ::1? I assume Bukkit doesn't allow you to IP ban the loopback address.

Is /minecraft:banip able to ban them successfully? I don't see any separation between Bukkit's IPv4 list and IPv6 list.

I looked into this issue, and as far as I can tell, there is nothing Essentials-side that would cause this. It's almost certainly an issue with Spigot.

As mentioned above, for those encountering this issue, please use /minecraft:banip. This is a workaround, but should work until Bukkit officially supports IPv6.