Almost all commands from this script are available in Essentials, not to mention you can write them by yourself within minutes, you can code "to-do list" in less than 15 minutes.
Instead of using one name for permissions, author decided to use different names EVERYWHERE, instead of one lobby.* You have to add all these permissions, one by one.
/setlobby command is pointless, don't even think it will teleport you to the place you set with that command.
Where is /chat off, /chat on marked as added here?: https://www.spigotmc.org/resources/lobby-system.94638/update?update=416039
This script seems stolen:
/gmc, /gms, /gma - https://www.spigotmc.org/resources/%E2%9C%94%EF%B8%8F-gamemode-command-shortcut-skript-%E2%9C%94%EF%B8%8F-1-9-1-16-%E2%9C%94%EF%B8%8F.84487/
Permissions: "gmc.use, gms.use, gma.use" - "gamemode.use"
Original:
"set the player's gamemode to creative
send "{@logo} &fGamemode set to &bCreative""
Stolen:
"set player's gamemode to creative
send "{@systeme} &aGamemode change to &bCreative""
/setlobby - https://forums.skunity.com/threads/spawn-system-help.12331/
Now you should know why /setlobby doesn't work. Author forgot to steal this piece of code:
"on join:
teleport player to {lobby}"
/cc - https://www.spigotmc.org/resources/clear-chat.90229/
You can clearly see "&aChat was cleared" in both files, where in original one, it also has "by &2%player%".
/day, /night - can't really tell, however this script is available in multiple posts and threads on multiple forums.

Summary: Use Essentials, or original scripts that are MUCH better.
Also, before author will start to blame me about how bad I am giving him 1 star review, look at yourself and people YOU gave bad reviews, without ANY explanations.