For some reason, Wipe Data Cleaner just ran for no reason. The server has been up for 3 hours, I didn't wipe it or anything.

Rust updated today, so perhaps because of that? This plugin is for automatically wiping when the server does, which it would have today.

Yeah could be, weird though as it happened almost 3 hours after I updated the server.
I've removed the plugin for now until I find out whats going on with it as it happened yesterday as well.

Plugin features are not triggered 'for no reason'.
There are exactly two possible reasons why it can be executed:

• OnNewSave hook was triggered (which happens while new save file is created which can only happen on server restart)
• Someone with permission (or from server console / rcon) ran 'wipe' command (this is what happened in your case I think)

Alright, well the server didn't restart. Unless there is an issue with the permissions and some random player typed /wipe

No players have permission to type the /Wipe command though 

Hi I'm still having issues with this, no players have permission to use the /Wipe command.
I am the only person who has access to the RCON and Server Console.

I don't know whether this could be a permission issue? Despite no players having access to the wipe permission.
Players type /Wipe to see the wipe schedule as some servers do this. If there was a permission issue that would explain it.

Also when this occurs it isn't when the server restarts it will just happen, not after a restart and we never mess with any save files.

Try the new update

Everything is working perfectly now, thanks for the help :)