Version: Latest non dev. 5.8.0
server is running CraftBukkit version git-Spigot-db6de12-18fbb24 (MC: 1.8.8) (Implementing API version 1.8.8-R0.1-SNAPSHOT)

Not only mutes and temp mutes can be assigned multiple times to the same user as it does not actually mute the player.

http://i.imgur.com/f52DXMZ.png

I also tried unloading my chat plugin to see if it was causing the issue but apparently its not (deluxechat)

Config: http://pastebin.com/ZjjFJkFp

Any errors in your console?

No. Console looks fine:
http://pastebin.com/T5PHU2ay when i run the command.

I think this is related to ban manager sometimes not being able to find a player, even tho he is online it's says player does not exist, this happens on occasion, but the mute thing is for everyone. essentials mute works fine muting players (altho very buggy) so I'm pretty sure is ban manager related.

Are you running in offline mode?

Yes.

BanManager does not support offline mode.

Well if thats true then having an "onlineMode: false" in the config doesn't make any sense.
If thats the case then i guess this ticket can be closed...
BTW i wouldn't mind dropping 20$+ for ban manager if it was a Premium Spigot plugin with at least "some" offline support, i am pretty sure many others would too.

@Done84 That was a community contribution but is indeed not officially supported by us. Also we don't accept payments for custom work on BanManager.

I wasn't offering a personal payment for custom work done. I was saying that if this had some sort of offline support it would sell many copies in the Spigot Premium (payd) Plugin Section since the only decent ban plugin has stopped being maintained. A 10 dollar plugin sold 300 times adds up pretty quickly, but your dev, your choice. Have a nice day sir.

Offline mode support could be enhanced by any other developer who has time to do that. As far as I know @confuser would be glad to merge those changes into BanManager but offline mode still won't be supported officially by BM/Frostcast.