My players have access to /plugins. They dont have the permission node. http://pastebin.com/WE0xZQPx

Which version of Minecraft and PEX are you running?

Your file has 1 user in it, and that 1 user is the owner, who has all permissions.

minecraft version is 1.8.8 and the plugin version is 1.23.4, and every player that does have all perms still has access to /plugins

You can try negating the Vanilla Permissions, but they are extremely random to control. (2 people running the exact same server may have different results.)

pex group <group> add -bukkit.command.plugins

Test the above command on your group(s). If it works— great! If it doesn't work, use Debug Mode:

1. Type pex user Stormbow toggle debug into the console to turn Debug Mode on.
2. Have Stormbow type /plugins in-game.
3. Type pex user Stormbow toggle debug into the console to turn Debug Mode off.
4. Look through the console output to find out which permission node(s) are giving Stormbow access to the /plugins command.
5. Negate those permission nodes with pex group <group> add -permission.node.name.

Do u need to join my server for debug mode?

nevermind thanks the first command worked

Do u need to join my server for debug mode?

You would (obviously) use your Minecraft name.

nevermind thanks the first command worked

Issue solved? You're welcome. :)