On my server, I am locked out of the plugin (I don't have access to the actual files, because the host is bad but doesn't cost anything). I seemingly am unable to set my permissions from the console. I also can't do anything period from the console.
I have tried adding a base permission, as well as a specific permission, but it all fails; as commands that are suposed to be dependant on those permissions fail with "Sorry, you don't have enough permissions". I have tried to enable all permissions for ops with /pex config permissions.enableOps true, followed by /pex reload, and also setting the permission with /pex user InfernoDeityInf add permissions.
(InfernoDeityInf is my username)
The attempts provided no feedback of any kind, and had no effect that was apparent.

NVM about not having access to the files, but I think that the console should do something, or at least provide some feedback.

Unfortunately PermissionsEx is currently unmaintained and no further updates are planned. Because of this, all issues are being closed. If you are looking for an actively maintained permissions plugin, take a look at LuckPerms. It is compatible with major server platforms and can import data from PEX.