Plugin Version: ItemJoin-5.0.7-SNAPSHOT-b491
Server Version: Paper 1.8.8

Console log: No console errors

Error desc: I can hold the interact button and execute the action two times

Okay, so the items-Spamming boolean was originally created to stop the spamming of items that were ItemCommands defined with a cooldown duration and a cooldown message. As well as items such as Ender Pearls to prevent spam right-clicking them all in a micro-second launching them all essentially at once.

I have now tweaked it so that it also prevents spamming items with commands defined without a cooldown or cooldown message. (I assume this was the issue you were having as you didn't provide your items.yml).

Please let me know if this resolves your problem; http://ci.craftationgaming.com/job/ItemJoin/498/

If it does not, please post your items.yml in a pastebin.com link and a clear description of how you are interacting with the item.

Let me know!

Solved

This bug has been officially fixed in the release of ItemJoin v5.0.7.
You can grab it here; Download: https://www.spigotmc.org/resources/itemjoin.12661/download?version=354306

Please read the changelog as the documentation has not been updated yet;
https://github.com/RockinChaos/ItemJoin/wiki/Recent-Changes