If you have items, that has the'inventory-modify' flag, located in the inventory (not in the hotbar), you are able to dupe said item when you Shift-Click on them. This make a copy of the item in the first available slot in the hotbar. Oh, this also works when hovering over the items and pressing 1-9 to relocate them.

This was tested on Spigot 1.8.8

I just discovered that the item dupe only happens in creative. However in survival you're still able to move items around using the 1-9 keys

screencap: https://im3.ezgif.com/tmp/ezgif-3-b995d1bd40.gif

items.yml: http://pastebin.com/W2NrzAvB
config.yml: http://pastebin.com/P42Q8Qkk

Ah... yeah... Sorry to say that its a bug within spigot/cb its self. I spent a while trying to figure this one out.
For the v4.0 recode I am trying to find a work around but its becoming difficult. I will keep you posted as I progress on this. (The creative dupe). The reason this happens btw is because for some reason player interacting with the inventory event gets triggered every 2nd time rather then every single time when in creative. Sadly no other inventory handle events work with this either, meaning they all also get triggered every 2nd time.

As for the 1-9 keys I found the issue I made it so you couldnt move them to your cursor but I never made it so you could make it so you cant move them from your cursor to your hotbar. Just had to add a simple reverse switch and its all fixed. Ill try to patch as much as I can and get a v3.9.3 bug fix out soon. I would like to find a temp fix for that creative mode issue tho.

Is it possible you can get me a screencap or link me to your server so I can test this out? I haven't seen this happen before.

Also a pastebin link to your items.yml and config.yml would be nice too.

Found a resolution and fixed both problems (however the inventory will still be force closed if you click a non moveable item while in creativemode only! this time without duping though.), just waiting on a proper time to update this for you.

Sorry for the late update, I have done somewhat of a "hacky" fix as it is a client-sided bug with mojang but it gets the overall job done. I will have to do a recode for v4.0 that involves sending the client packets, that would probably have a better outcome, anyways it has been released and you can get it here;

https://www.spigotmc.org/resources/itemjoin.12661/download?version=152238