So this error was from the upgrade from 1.7.5 to 1.7.9 and that fact that we use spigot. I was having errors updating the player file and while I reverted the version the player files were still acting up.
The problem was that we had over 1,000 users in our player file and the Minecraft servers were only allowing us to update 500 at a time with spigot.
I was able to fix the problem by starting a vanilla Minecraft server with the player file in a blank world. When Minecraft started it updated the player.dat files. Then I stopped the server and moved the new player files into our world with spigot and restarted.
Now we have all servers running version 1.7.9 and the error should not come up anymore.