When you type /clan, or any other commands that this plugin provides only once, it goes through 4-5 times.

Nope. It just does that.

After the aliases update. To be exact.

Did you by any chance /reload 4-5 times?

Very odd, this happened to me once but could not replicate it. I am using the onPlayerCommandPreprocess event, and not cancelling it if it was cancelled. So that may be the problem. I have added code to 1.3.3 to exit if the event was cancelled, lets see if this fixes your problem.

Reopen if not fixed