BLANKET STATEMENT: I've never made my own server before. MCMMO Vault Essentials X 2.0.1 CrazyEnchantments Towny Shop bPermissions 2.12 Jobs 3.6.3 Vault Ran by spigot. If someone isn't OPed they can't use commands of really any kind. The only things that work without issue is jobs, mcmmo and towny. I really don't know where to start fixing this. And there are not enough youtube tutorials in the world to help me do this. The dev pages are less than helpful most of them and no one irl that I know has a clue.
Since you haven't much experience with bPermissions I'd like to suggest that you switch to PermissionsEx as it's better documented and has far more tutorials on YouTube.
Considering I didn't post what edition my server was I'll chill out. The server is 1.10 but if you looked at the stuff I listed off by edition you would've seen that. Permissions ex goes to 1.9 so that is completely out of the question.
@NyxSilence Your point? I have plugins that I made for 1.7 that still work on 1.10. PermissionsEx still works perfectly on 1.10 as far as I've seen. It'd be a good idea to check it out. Personally I prefer GroupManager but that is outdated & doesn't work anymore.