1.) ItemJoin v5.0.1
2.) CraftBukkit version git-Spigot-518206a-a5b9c7b (MC: 1.13.2) (Implementing API version 1.13.2-r0.1-SNAPSHOT)
3.) Everytime that I set "%player%" in the "skull-owner" the item stops working. I still receive it, but commands and itemflags still dont working.
4.) https://pastebin.com/0ngfCjFj
skull:
id: PLAYER_HEAD
slot: 3
name: 'Test'
skull-owner: '%player%'
lore:
- '&7Great for setting a'
- '&7players profile, like hypixel!'
commands:
multi-click:
- 'message: &cOkay!'
itemflags: inventory-modify, death-drops, self-drops, item-store, death-drops, self-drops, cancel-events, placement
triggers: join, respawn, world-change
enabled-worlds: Spawn

(Nice plugin buddy <3)

Issue should be resolved in the latest snapshot; http://ci.craftationgaming.com/job/ItemJoin/182/

Please let me know!

The "dynamic" problem remains.

I apologize, it looks like the spigot API changed with how it handles delays.
I have tested it as working in the latest snapshot; http://ci.craftationgaming.com/job/ItemJoin/184/

It's working! Thanks :)

I don't know why, but the dynamic itnes don't refresh.
gadget:
id: ENDER_CHEST
slot: 4
name: '&aGeneric text'
lore:
- 'delay:20&7Mystery Dust: &b%gadgetsmenu_mystery_dust%'
- '&7Mystery Box: &b%gadgetsmenu_mystery_boxes%'
commands:
multi-click:
- 'gmenu main'
commands-type: interact, inventory
commands-sequence: SEQUENTIAL
itemflags: dynamic, inventory-modify, death-drops, self-drops, item-store, count-lock, death-drops, self-drops, inventory-modify, cancel-events, placement, item-repairable, item-craftable, hide-attributes
triggers: join, respawn, world-change
enabled-worlds: Lobby

I set another placeholders but still don't refreshing.

My apologies, I have fixed this in the latest snapshot; http://ci.craftationgaming.com/job/ItemJoin/183/

Still the same bug. Can it be my version of spigot?

You set up the item incorrectly.

When you add a delay it should look like this;
<delay:20>

so it should look like;
lore:
- '<delay:20>&7Mystery Dust: &b%gadgetsmenu_mystery_dust%'

Although that a little weird that it's not working because I copied the exact item you had above except I replaced the placeholder to test the delay properly.

I am using 1.13.2 (The same version as you) and it is working as intended. (Updating the item's lore every 20 ticks (1 second) keeping the time going up as normal.)
Are you sure you are using the item you provided above?

EDIT: Make sure you are actually using the snapshot and that you don't have duplicate ItemJoin jar files in your server plugins folder. The release jar vs the snapshot jar file is different names so it's easy to put both in your plugins folder by accident. (When this happens it usually uses the original release version when booting the server).

I set up a new server to test it but still the same bug. I think it's my spigot

1. https://imgur.com/2MfpAP5
2. https://imgur.com/qaHuHjc
3. https://imgur.com/uCOZFSY
4. https://imgur.com/rHpEPuN

Okay so I downgraded to the EXACT version (build #) of Spigot 1.13.2 you are using; CraftBukkit version git-Spigot-518206a-a5b9c7b (MC: 1.13.2) (Implementing API version 1.13.2-r0.1-SNAPSHOT)

And it is still working for me.
I also used the images you provided me to produce an exact replica of the situation;

Here is a video to confirm working;
https://i.imgur.com/SokLPOy.mp4

I am still not convinced that you are using the fixed ItemJoin snapshot (meaning a mix-up of which jar file is which) as it doesn't matter what spigot api you are using, I tested it from 1.7-1.13.2 and I can confirm working.

Can you try to delete the ItemJoin far file in your plugins folder and download this latest snapshot; http://ci.craftationgaming.com/job/ItemJoin/186/

I downloaded the latest snapshot version as I was doing it before and it worked now (Build #186). Sorry about your hard work and thank you for your help.
By the way, sorry for my bad english. Have a nice day :)

Its all good I am glad I was able to help. If you need any more help feel free to let me know!

This issue has been officially fixed in the release of ItemJoin v5.0.2.
You can grab it here; https://www.spigotmc.org/resources/itemjoin.12661/download?version=258611

Please read the changelog as the documentation has not been updated yet;
https://www.spigotmc.org/wiki/recent-changes