I set Prefix: ''

And it it still showing the prefix in chat. Bug?

I did a quick test and it seems to be working just fine, no prefix for me.
Are you talking about item cooldown's or what exactly is the action you are doing that is causing the message to appear and what is the message?
Don't forget the cooldown messages are stored with a prefix already in the items.yml so if any items have a cool-down message it will appear with the prefix unless you remove it from the actual message within the items.yml.

yea, I am talking about the item cooldown's prefix and thank you for pointing that out. the issue is solved.