Everytime I want to invite someone to my clan [I'm the server owner.] it says "The Player doesn't not [doesn't not? Wow.] have the permissions to join clans". I'd have to OP everyone in order to invite them but you probably understand that I can't do that. Also after I deop them when they're in, they are basically not able to do anything. Is there something I am missing out on? Any help will be appreciated.

What Permissions plugin do you use? Let me see its files. Or at least list the permissions related to SimpleClans that your players own.

I am using PermissionsEX but do not know how to use it for other plugins.
And I'm not experienced with it at all.

So you did not give SimpleClans permissions to the players...?

I took a look into the config.yml file but could not find something that'd help with that.

Read this guide:
https://github.com/PEXPlugins/PermissionsEx/wiki/Basic-Permissions-Setup

I am closing this issue, it does not seem to be a SimpleClans bug. Reopen if you think is necessary.