I have created a fresh install of spigot 1.13.2, I have several servers on a waterfall (bungeecord) network and had no issues with luckperms before. Unless i am op'ed I cant use any command. I have verified that the server name in LP config and server name used for commands are the same. I have included all the info I can think to add about the server. All the screenshots are just as a proof thing showing that I didn't screw that part up.

Here is some verbose. I had the player de-op'ed and try to run gm commands. He had 3 perms for the "aquatic" server where this is happening. luckperms.* minecraft.* and *. He should have everything now but still can't run /gm 0. Here is the verbose during that.
https://luckperms.github.io/verbose/#yEkj52YcD0
I then gave him essentials.* and tried again. Verbose for that
https://luckperms.github.io/verbose/#wang0P177K
I verified that I'm not removing essentials.* anywhere
https://drive.google.com/file/d/1Sbly_FMIsWuNBpVMXJoUu2QjK6g488Xf/view

Screenshots showing the results of /lpb user username info and /lp user username info
/lpb https://drive.google.com/file/d/1PnmsLWZbRS-KbVxdguCG2yxKsoTl3-3I/view
/lp https://drive.google.com/file/d/1mUxii9ZHYSUCU_OfA3wTxJXVzIcinLX8/view
The uuid's are good, I set up that part right.

It doesn't matter what the perm is or what groups/users I give them to, LP just won't say the user can run the commands.

My current plugin list:
spigot-1.13.2
worldguard-legacy-7.0.0-beta01.jar
worldedit-bukkit-7.0.0-beta-01.jar
Vault.jar
UltimateChat-JDA.jar
UltimateChat-1.8.8-b200-Universal.jar
Ridables.jar
mcMMO.jar
LuckPerms-Bukkit-4.3.25.jar
GriefPrevention.jar
EssentialsXSpawn-2.15.0.55.jar
EssentialsX-2.15.0.55.jar
CoreProtect-2.15.1.jar
BungeeTabListPlus_BukkitBridge-2.8.9.jar

Current LP config, in case I screwed something up in there.
https://hastebin.com/anuseroven.shell

You should set a messaging service (since you're using MySQL you can use sql) to make changes apply on all servers.

Is that not default when using MySQL?

# - Possible options:
#   => sql       Uses the SQL database to form a queue system for communication. Will only work when
#                'storage-method' is set to MySQL or MariaDB. This is chosen by default if the
#                option is set to 'none' and SQL storage is in use. Set to 'notsql' to disable this.

This is the only server that has a version of LP with a sql option for messaging service. Once I get this set up im going to move them all to redis. It looks like redis is the only option between all versions of LP that I'm running.

You have set include-global and include-global-world to false in your config, that's your problem.

As for messaging service, you really don't need to use Redis unless you have multiple Bungeecord instances. sql is the best option there and you're right in that it does default to that if it's set to none, though I'd set it to sql just in case. If your config files don't mention it then they are probably outdated.

... You have any idea how annoying it is that one little config setting that i over looked is the reason that 3 different people couldn't fix this. One of them being an Unlucky (MOD) from discord. Thank you, include-global-world should have been set to true. Include-global should be set to false for my use. The version of LP that I have loaded on all the other servers are old. They were established a while back and haven't had a need to update yet. That's why there is no sql config option for messaging service.

Thank you for figuring it out.